packages: Use 'lookup-package-input' and friends instead of 'package-input'.

* guix/packages.scm (package-input, package-native-input): Remove. (this-package-input): Use 'lookup-package-input' and 'lookup-package-propagated-input' instead of 'package-input'. (this-package-native-input): Use 'lookup-package-native-input' instead of 'package-input'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
author: Maxime Devos <maximedevos@telenet.be> 2021-07-19 11:08:40 +0200
committer: Ludovic Courtès <ludo@gnu.org> 2021-07-23 10:51:57 +0200
commit: d7942ac12ad51615cd43d3debb8b561a503e8fc0 (patch)
tree: 25ef7f939eb7dd24d4dca7c8c12af2e1091b5bbc /gnu/packages/patches/audiofile-fix-sign-conversion.patch
parent: 93a5e89008af440655527d03d62d4726683a89ac (diff)
download: guix-d7942ac12ad51615cd43d3debb8b561a503e8fc0.tar.gz
guix-d7942ac12ad51615cd43d3debb8b561a503e8fc0.zip
0 files changed, 0 insertions, 0 deletions
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 531686fdbb..48b9c8b893 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1162,14 +1162,14 @@ connection alive.")
                                       bind-release-version)))
     (package
       (name "isc-dhcp")
-      (version "4.4.2")
+      (version "4.4.2-P1")
       (source (origin
                 (method url-fetch)
                 (uri (string-append "https://ftp.isc.org/isc/dhcp/"
                                     version "/dhcp-" version ".tar.gz"))
                 (sha256
                  (base32
-                  "08a5003zdxgl41b29zjkxa92h2i40zyjgxg0npvnhpkfl5jcsz0s"))))
+                  "06jsr0cg5rsmyibshrpcb9za0qgwvqccashdma7mlm1rflrh8pmh"))))
       (build-system gnu-build-system)
       (arguments
        `(#:parallel-build? #f
@@ -1292,7 +1292,7 @@ connection alive.")
                 ("coreutils*" ,coreutils)
                 ("sed*" ,sed)))
 
-      (home-page "https://www.isc.org/products/DHCP/")
+      (home-page "https://www.isc.org/dhcp/")
       (synopsis "Dynamic Host Configuration Protocol (DHCP) tools")
       (description
        "ISC's Dynamic Host Configuration Protocol (DHCP) distribution provides a
@@ -3608,14 +3608,14 @@ information tool.")
 (define-public nnn
   (package
     (name "nnn")
-    (version "4.0")
+    (version "4.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/jarun/nnn/releases/download/v"
                            version "/nnn-v" version ".tar.gz"))
        (sha256
-        (base32 "0m07nh1cdfikn4bkpni29j61hr9jdwbl0n5fmlm53l1xmn7yq6d2"))))
+        (base32 "1fnf35s3b2nfp18s712n5vhg6idx4rfgwdfv74nc2933v9l2dq7h"))))
     (build-system gnu-build-system)
     (inputs
      `(("ncurses" ,ncurses)
@@ -3626,30 +3626,26 @@ information tool.")
      `(#:tests? #f                      ; no tests
        #:phases
        (modify-phases %standard-phases
-         (delete 'configure)            ; no configure script
-         (add-after 'unpack 'patch-pkg-config
-           (lambda _
-             (substitute* "Makefile"
-               (("pkg-config")
-                ,(pkg-config-for-target))))))
+         (delete 'configure))           ; no configure script
        #:make-flags
        (list
         (string-append "PREFIX="
                        (assoc-ref %outputs "out"))
-        (string-append "CC=" ,(cc-for-target)))))
+        (string-append "CC=" ,(cc-for-target))
+        (string-append "PKG_CONFIG=" ,(pkg-config-for-target)))))
     (home-page "https://github.com/jarun/nnn")
     (synopsis "Terminal file browser")
-    (description "@command{nnn} is a fork of @command{noice}, a blazing-fast
-lightweight terminal file browser with easy keyboard shortcuts for
-navigation, opening files and running tasks.  There is no config file and
-mime associations are hard-coded.  The incredible user-friendliness and speed
-make it a perfect utility on modern distros.")
+    (description
+     "@command{nnn} is a fork of @command{noice}, a fast and minimal text
+terminal file browser with keyboard shortcuts for navigation, opening files and
+running tasks.  There is no configuration file and MIME associations are
+hard-coded.")
     (license license:bsd-2)))
 
 (define-public thermald
   (package
     (name "thermald")
-    (version "2.4.4")
+    (version "2.4.5")
     (source
      (origin
       (method git-fetch)
@@ -3658,7 +3654,7 @@ make it a perfect utility on modern distros.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "1k0r2c13fihjndwfh0byw0i8ni4lzsjgwz874pvpj1l1nvjj0ajx"))))
+       (base32 "1y8s0cpjm01bz4isp3ksvnrbhpp3phivdhsb0w2kxhv09sfxkc5g"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -3672,13 +3668,7 @@ make it a perfect utility on modern distros.")
        (modify-phases %standard-phases
          (add-before 'bootstrap 'no-early-./configure
            (lambda _
-             (setenv "NO_CONFIGURE" "yet")
-             ;; XXX thd_trip_point.h redefines "__STDC_LIMIT_MACROS" after
-             ;; <xz>/include/lzma.h.  ./configure forcibly appends -Werror
-             ;; to CXXFLAGS, overriding any -Wno-error we'd add.
-             (substitute* "configure.ac"
-               (("-Werror") ""))
-             #t)))))
+             (setenv "NO_CONFIGURE" "yet"))))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("autoconf-archive" ,autoconf-archive)
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index a4d3f5ac68..d0312426d0 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -341,7 +341,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "1.7.0-9")
+    (version "1.7.0-11")
     (source
      (origin
        (method url-fetch)
@@ -353,7 +353,7 @@ precision.")
                            "~parisse/debian/dists/stable/main/source/"
                            "giac_" version ".tar.gz"))
        (sha256
-        (base32 "0yl5h13rnis8gqg48g9z719d5xfgxjcxz7bwbdqlwsvdy42crrim"))))
+        (base32 "12njy2akcc3sj1fmq52v19m4qd1ysrdcpc9a3zslkxsnidjix81m"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
diff --git a/gnu/packages/animation.scm b/gnu/packages/animation.scm
index 3a915c7fda..71fc8f20b0 100644
--- a/gnu/packages/animation.scm
+++ b/gnu/packages/animation.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Pkill -9 <pkill9@runbox.com>
-;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,10 +25,12 @@
   #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages assembly)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
@@ -45,6 +47,8 @@
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages jemalloc)
+  #:use-module (gnu packages networking)
+  #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
@@ -320,6 +324,78 @@ audio or video backends, ensuring good performance.")
       (home-page "https://www.gnu.org/software/gnash/")
       (license license:gpl3+))))
 
+;; This package provides a standalone (no browser plugin) version of
+;; Lightspark.
+(define-public lightspark
+  (package
+    (name "lightspark")
+    (version "0.8.4.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/lightspark/lightspark")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "17l5gzb7p8nivx1a2frca2jklcjdsk2qj4jniv3z8bh307ksz254"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f ;requires Adobe Flex SDK, see README.tests
+       ;; Disable browser plugins because neither NPAPI nor PPAPI is
+       ;; supported in the browsers we have.
+       #:configure-flags
+       '("-DCOMPILE_NPAPI_PLUGIN=FALSE"
+         "-DCOMPILE_PPAPI_PLUGIN=FALSE")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'prepare-build-environment
+           (lambda _
+             ;; Use relative etc path.
+             (substitute* "CMakeLists.txt" (("\\/etc") "etc"))))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "./tests")))))))
+    (native-inputs
+     `(("gettext" ,gettext-minimal)
+       ("glib:bin" ,glib "bin")
+       ("nasm" ,nasm)
+       ("perl" ,perl)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python-wrapper)))
+    (inputs
+     `(("cairo" ,cairo)
+       ("curl" ,curl)
+       ("ffmpeg" ,ffmpeg)
+       ("freeglut" ,freeglut)
+       ("glew" ,glew)
+       ("glibmm" ,glibmm)
+       ("gnash" ,gnash)
+       ("gnutls" ,gnutls)
+       ("libjpeg" ,libjpeg-turbo)
+       ("openssl" ,openssl)
+       ("pango" ,pango)
+       ("pcre2" ,pcre2)
+       ("rtmpdump" ,rtmpdump)
+       ("sdl2" ,sdl2)
+       ("sdl2-mixer" ,sdl2-mixer)
+       ("zlib" ,zlib)))
+    (home-page "https://lightspark.github.io/")
+    (synopsis "Flash player implementation")
+    (description
+     "Lightspark is a Flash player implementation for playing files in the SWF
+format.  It supports SWF files written on all versions of the ActionScript
+language.")
+    ;; NOTE: The bundled pugixml is a fork specific to Lightspark and
+    ;; incompatible with the one we have.
+    ;; FIXME: we also have jxrlib, but the build fails to find JXRMeta.h so we
+    ;; use the bundled one for now.
+    (license (list license:lgpl3+ ;lightspark
+                   license:mpl2.0 ;avmplus
+                   license:bsd-2 ;jxrlib
+                   license:expat)))) ;pugixml, PerlinNoise
+
 (define-public papagayo
   (let ((commit "e143684b30e59fe4a554f965cb655d23cbe93ee7")
         (revision "1"))
diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm
index e19c369517..a86984b28c 100644
--- a/gnu/packages/aspell.scm
+++ b/gnu/packages/aspell.scm
@@ -489,14 +489,14 @@ under permissive licensing terms.  See the 'Copyright' file."))))
 (define-public ispell
   (package
     (name "ispell")
-    (version "3.4.02")
+    (version "3.4.04")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.cs.hmc.edu/~geoff/tars/ispell-"
                            version ".tar.gz"))
        (sha256
-        (base32 "0b6rqzqjdhwf323sf1dv8qzx5pxa5asz618922r59zjp65660yb6"))))
+        (base32 "0gp1rwn8grkvz28wgisc2j9w9svldnaiahl3lyis118xabqddg47"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6d1c4ddfe6..c4a686957d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -228,7 +228,7 @@ astronomical image-processing packages like Drizzle, Swarp or SExtractor.")
 (define-public gnuastro
   (package
     (name "gnuastro")
-    (version "0.14")
+    (version "0.15")
     (source
      (origin
        (method url-fetch)
@@ -236,7 +236,7 @@ astronomical image-processing packages like Drizzle, Swarp or SExtractor.")
                            version ".tar.lz"))
        (sha256
         (base32
-         "1xp6n42qxv0x6yigi2w2l5k8006smv27lhrcssysgsvzbydghzg5"))))
+         "1jjr3ixxbpsr5m4s7ahh12ymcnlvjzwcp02ya16b1lvzrz1wmhy4"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--disable-static")))
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 930c111d5e..b250bc3af0 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -302,7 +302,7 @@ Linux kernel.")
 (define-public libopenmpt
   (package
     (name "libopenmpt")
-    (version "0.5.8")
+    (version "0.5.9")
     (source
      (origin
        (method url-fetch)
@@ -310,7 +310,7 @@ Linux kernel.")
         (string-append "https://download.openmpt.org/archive/libopenmpt/src/"
                        "libopenmpt-" version "+release.autotools.tar.gz"))
        (sha256
-        (base32 "1kca5nc870mfv7i4ww2g1q9jn61gsq46irsypbr6fgxpfh8w5qi9"))))
+        (base32 "0h86p8mnpm98vc4v6jbvrmm02fch7dnn332i26fg3a2s1738m04d"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -1022,7 +1022,7 @@ generators of mostly elementary and occasionally exotic nature.")
 (define-public infamous-plugins
   (package
     (name "infamous-plugins")
-    (version "0.2.04")
+    (version "0.3.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1031,7 +1031,7 @@ generators of mostly elementary and occasionally exotic nature.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0hmqk80w4qxq09iag7b7srf2g0wigkyhzq0ywxvhz2iz0hq9k0dh"))))
+                "1r72agk5nxf5k0mghcc2j90z43j5d9i7rqjmf49jfyqnd443isip"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests
@@ -1041,6 +1041,12 @@ generators of mostly elementary and occasionally exotic nature.")
            (lambda _
              (substitute* (find-files "." "CMakeLists.txt")
                (("-msse2 -mfpmath=sse") ""))
+             #t))
+         (add-after 'unpack 'fix-build-with-newer-lv2
+           (lambda _
+             ;; https://github.com/ssj71/infamousPlugins/commit/4c7275b1fa8ea3296446421cbd29ec2df66588c0
+             (substitute* (find-files "src" ".*\\.cxx")
+               (("_LV2UI_Descriptor") "LV2UI_Descriptor"))
              #t)))))
     (inputs
      `(("cairo" ,cairo)
@@ -4313,7 +4319,7 @@ representations.")
 (define-public cava
   (package
     (name "cava")
-    (version "0.7.3")
+    (version "0.7.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -4322,7 +4328,7 @@ representations.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "04j5hb29hivcbk542sfsx9m57dbnj2s6qpvy9fs488zvgjbgxrai"))))
+                "1mziklmqifhnb4kg9ia2r56r8wjn6xp40bkpf484hsgqvnrccl86"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("autoconf" ,autoconf)
@@ -4465,7 +4471,7 @@ library.")
 (define-public faudio
   (package
     (name "faudio")
-    (version "21.05")
+    (version "21.06")
     (source
      (origin
        (method git-fetch)
@@ -4474,7 +4480,7 @@ library.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0lzvfx5gg5m6jbdzqwkjl4wq4fdg5n98fxn5x8n65vgvrj95sx6z"))))
+        (base32 "1nnx4l1r5hwdaw824d4fmd558qsqa22qzpvnkhs8nkjr40cnidkr"))))
     (arguments
      '(#:tests? #f                      ; No tests.
        #:configure-flags '("-DGSTREAMER=ON")))
@@ -5165,14 +5171,18 @@ while still staying in time.")
 (define-public butt
   (package
     (name "butt")
-    (version "0.1.29")
+    (version "0.1.30")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/butt/butt/butt-"
                                   version "/butt-" version ".tar.gz"))
               (sha256
                (base32
-                "0nbz0z4d7krvhmnwn10594gwc61gn2dlb5fazmynjfisrfdswqlg"))))
+                "1dfspdh3f18lpp7asxpj63b9zfpvazi7shgrdacg17gd42ycayq5"))
+              (modules '((guix build utils)))
+              (snippet
+               '(substitute* "src/butt.cpp"
+                  ((".*zica.*") "")))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -5209,7 +5219,7 @@ while still staying in time.")
                                         version "_manual.pdf"))
                     (sha256
                      (base32
-                      "1hhgdhdg5s86hjcbwh856gcd3kcch0i5xgi3i3v02zz3xmzl7gg3"))))))
+                      "1w3krh7f2v5vdz18hqycnpn0qv1x6xl6pa1najgp4jbfisjc1mn8"))))))
     (home-page "https://danielnoethen.de/butt/")
     (synopsis "Audio streaming tool")
     (description "Butt is a tool to stream audio to a ShoutCast or
diff --git a/gnu/packages/axoloti.scm b/gnu/packages/axoloti.scm
index 0b12e4fe29..c6dd748773 100644
--- a/gnu/packages/axoloti.scm
+++ b/gnu/packages/axoloti.scm
@@ -125,6 +125,11 @@
                (("arm-none-eabi-(gcc|g\\+\\+|objcopy|objdump)" tool)
                 (which tool)))
 
+             ;; XXX: for some reason the whitespace substitution does not
+             ;; work, so we disable it.
+             (substitute* "firmware/Makefile.patch"
+               (("^BDIR=.*") "BDIR=${axoloti_home}/build\n"))
+
              ;; Hardcode full path to compiler tools
              (substitute* '("firmware/Makefile"
                             "firmware/flasher/Makefile"
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index a537cd46f3..6a6ac1d8d5 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2019 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2019, 2021 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2020 malte Frank Gerdes <malte.f.gerdes@gmail.com>
 ;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@@ -52,14 +52,14 @@
 (define-public fio
   (package
     (name "fio")
-    (version "3.26")
+    (version "3.27")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://brick.kernel.dk/snaps/"
                                   "fio-" version ".tar.bz2"))
               (sha256
                (base32
-                "1114h60vw63bim872an33xpvjfib6sc9dwj9xvk0yw41xjzfpp06"))))
+                "0akaixip86ycbxr13bjff2121rgfbz35fa9l39677wpwzckp4f4d"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"
@@ -126,13 +126,9 @@ is to write a job file matching the I/O load one wants to simulate.")
     (license (list license:gpl2 license:gpl2+ license:bsd-2
                    license:public-domain))))
 
-;; Parameterized in anticipation of m(va)pich support
-(define (intel-mpi-benchmarks mpi)
+(define-public intel-mpi-benchmarks/openmpi
   (package
-    (name (string-append "intel-mpi-benchmarks"
-                         (if (string=? (package-name mpi) "openmpi")
-                             ""
-                             (string-append "-" (package-name mpi)))))
+    (name "intel-mpi-benchmarks")
     (version "2019.6")
     (source (origin
               (method git-fetch)
@@ -154,7 +150,7 @@ is to write a job file matching the I/O load one wants to simulate.")
                   #t))))
     (build-system gnu-build-system)
     (inputs
-     `(("mpi" ,mpi)))
+     `(("openmpi" ,openmpi)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -194,9 +190,6 @@ Efficiency of the MPI implementation.
 @end itemize")
     (license license:cpl1.0)))
 
-(define-public intel-mpi-benchmarks/openmpi
-  (intel-mpi-benchmarks openmpi))
-
 (define-public imb-openmpi
   (deprecated-package "imb-openmpi" intel-mpi-benchmarks/openmpi))
 
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 45e31a5760..d84481bdb8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,15 +1,16 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
+;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -35,8 +36,10 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages graph)
   #:use-module (gnu packages graphviz)
@@ -103,6 +106,29 @@ analysis.")
 database, assembled using data from REACTOME.")
     (license license:cc-by4.0)))
 
+(define-public r-bsgenome-btaurus-ucsc-bostau8
+  (package
+    (name "r-bsgenome-btaurus-ucsc-bostau8")
+    (version "1.4.2")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8"
+                                     version 'annotation))
+              (sha256
+               (base32
+                "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"))))
+    (properties
+     `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bsgenome" ,r-bsgenome)))
+    (home-page
+     "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
+    (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
+    (description "This package provides the full genome sequences for Bos
+taurus (UCSC version bosTau8).")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome-celegans-ucsc-ce6
   (package
     (name "r-bsgenome-celegans-ucsc-ce6")
@@ -412,6 +438,28 @@ in Biostrings objects.")
 ID and species.  It is used by functions in the GenomeInfoDb package.")
     (license license:artistic2.0)))
 
+(define-public r-go-db
+  (package
+    (name "r-go-db")
+    (version "3.7.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GO.db" version 'annotation))
+              (sha256
+               (base32
+                "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
+    (properties
+     `((upstream-name . "GO.db")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)))
+    (home-page "https://bioconductor.org/packages/GO.db")
+    (synopsis "Annotation maps describing the entire Gene Ontology")
+    (description
+     "The purpose of this GO.db annotation package is to provide detailed
+information about the latest version of the Gene Ontologies.")
+    (license license:artistic2.0)))
+
 (define-public r-homo-sapiens
   (package
     (name "r-homo-sapiens")
@@ -934,6 +982,64 @@ datasets which are derived from the Allen Brain Atlas:
 All datasets are restricted to protein coding genes.")
     (license license:gpl2+)))
 
+(define-public r-aneufinderdata
+  (package
+   (name "r-aneufinderdata")
+   (version "1.18.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "AneuFinderData" version 'experiment))
+            (sha256
+             (base32
+              "02vb3kmza5hv8bc424fdmfif608xvpdb759w8882kac8izpv29ks"))))
+   (build-system r-build-system)
+   (home-page "https://bioconductor.org/packages/AneuFinderData/")
+   (synopsis "Data package for @code{AneuFinder}")
+   (description "This package contains data used by @code{AneuFinder}.")
+   (license license:artistic2.0)))
+
+(define-public r-aneufinder
+  (package
+    (name "r-aneufinder")
+    (version "1.20.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AneuFinder" version))
+              (sha256
+               (base32
+                "0m6wphlriq7y21ih1p2kzml5jzcic79jc52kkk59dkjj8j88yllk"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (propagated-inputs
+     `(("r-genomicranges" ,r-genomicranges)
+       ("r-aneufinderdata" ,r-aneufinderdata)
+       ("r-ecp" ,r-ecp)
+       ("r-foreach" ,r-foreach)
+       ("r-doparallel" ,r-doparallel)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-bamsignals" ,r-bamsignals)
+       ("r-dnacopy" ,r-dnacopy)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-reshape2" ,r-reshape2)
+       ("r-ggdendro" ,r-ggdendro)
+       ("r-ggrepel" ,r-ggrepel)
+       ("r-reordercluster" ,r-reordercluster)
+       ("r-mclust" ,r-mclust)
+       ("r-cowplot" ,r-cowplot)))
+    (home-page "https://bioconductor.org/packages/AneuFinder/")
+    (synopsis "Copy number variation analysis in single-cell-sequencing data")
+    (description "This package implements functions for copy number variant
+calling, plotting, export and analysis from whole-genome single cell
+sequencing data.")
+    (license license:artistic2.0)))
+
 (define-public r-arrmdata
   (package
     (name "r-arrmdata")
@@ -974,6 +1080,30 @@ from Illumina 450k methylation arrays.")
 chromstaR package.")
     (license license:gpl3)))
 
+(define-public r-copyhelper
+  (package
+    (name "r-copyhelper")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
+       (sha256
+        (base32
+         "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
+    (properties `((upstream-name . "CopyhelpeR")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/CopyhelpeR/")
+    (synopsis "Helper files for CopywriteR")
+    (description
+     "This package contains the helper files that are required to run the
+Bioconductor package CopywriteR.  It contains pre-assembled 1kb bin GC-content
+and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
+mm10.  In addition, it contains a blacklist filter to remove regions that
+display copy number variation.  Files are stored as GRanges objects from the
+GenomicRanges Bioconductor package.")
+    (license license:gpl2)))
+
 (define-public r-genelendatabase
   (package
     (name "r-genelendatabase")
@@ -998,6 +1128,32 @@ chromstaR package.")
 genomes and gene ID formats, largely based on the UCSC table browser.")
     (license license:lgpl2.0+)))
 
+(define-public r-genomationdata
+  (package
+    (name "r-genomationdata")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "genomationData" version 'experiment))
+              (sha256
+               (base32
+                "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
+    (properties
+     `((upstream-name . "genomationData")))
+    (build-system r-build-system)
+    ;; As this package provides little more than large data files, it doesn't
+    ;; make sense to build substitutes.
+    (arguments `(#:substitutable? #f))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+    (synopsis "Experimental data for use with the genomation package")
+    (description
+     "This package contains experimental genetic data for use with the
+genomation package.  Included are Chip Seq, Methylation and Cage data,
+downloaded from Encode.")
+    (license license:gpl3+)))
+
 (define-public r-pasilla
   (package
     (name "r-pasilla")
@@ -1165,14 +1321,14 @@ across the entire multi-'omics experiment.")
 (define-public r-biocversion
   (package
     (name "r-biocversion")
-    (version "3.12.0")
+    (version "3.13.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocVersion" version))
        (sha256
         (base32
-         "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
+         "0rsw8g4g1pcjw1zbx8x17yd3drhxqk4sx3cy3ddzy5731hl6mbfi"))))
     (properties `((upstream-name . "BiocVersion")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BiocVersion/")
@@ -1185,13 +1341,13 @@ of Bioconductor.")
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.36.1")
+    (version "0.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "0x8cllriayrs99wd5l003iq6i28rb1mci23qcn13ga85578f5lz5"))))
+                "1kv7lzmyki3hi771v01nml1v1hzz8pyhqqv0xcdzqy354mlgx4m6"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
@@ -1205,13 +1361,13 @@ packages.")
 (define-public r-coverageview
   (package
     (name "r-coverageview")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "CoverageView" version))
               (sha256
                (base32
-                "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
+                "1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-s4vectors" ,r-s4vectors)
@@ -1232,13 +1388,13 @@ how the coverage distributed across the genome.")
 (define-public r-cummerbund
   (package
    (name "r-cummerbund")
-   (version "2.32.0")
+   (version "2.34.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "cummeRbund" version))
              (sha256
               (base32
-               "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
+               "1avvmvrmldbscc7xd6a6k22xjykbzafvqf87wh5z9rx3qlzswsjx"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
@@ -1259,16 +1415,76 @@ data.  In addition, provides numerous plotting functions for commonly
 used visualizations.")
    (license license:artistic2.0)))
 
+(define-public r-decipher
+  (package
+    (name "r-decipher")
+    (version "2.20.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "DECIPHER" version))
+              (sha256
+               (base32
+                "0mr7glkx2d37l9nszs52m0kycpm14vxl5gdp3z7i5j7yig1sw2nk"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-dbi" ,r-dbi)
+       ("r-iranges" ,r-iranges)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://www.bioconductor.org/packages/DECIPHER/")
+    (synopsis "Tools for deciphering and managing biological sequences")
+    (description "This package provides a toolset for deciphering and managing
+biological sequences.")
+    (license license:gpl3)))
+
+(define-public r-deepsnv
+  (package
+    (name "r-deepsnv")
+    (version "1.38.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "deepSNV" version))
+              (sha256
+               (base32
+                "0zz56hf417m7bgg2g2wpbaik30pi6h2nam1n5bviqgdn4mv8n0bs"))))
+    (properties `((upstream-name . "deepSNV")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)
+       ("r-vgam" ,r-vgam)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/gerstung-lab/deepSNV/")
+    (synopsis "Detection of subclonal SNVs in deep sequencing data")
+    (description
+     "This package provides quantitative variant callers for detecting
+subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
+The deepSNV algorithm is used for a comparative setup with a control experiment
+of the same loci and uses a beta-binomial model and a likelihood ratio test to
+discriminate sequencing errors and subclonal SNVs.  The shearwater algorithm
+computes a Bayes classifier based on a beta-binomial model for variant calling
+with multiple samples for precisely estimating model parameters - such as local
+error rates and dispersion - and prior knowledge, e.g.  from variation data
+bases such as COSMIC.")
+    (license license:gpl3)))
+
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.16.3")
+    (version "0.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "0w1wppy6m2iv41852dscg3y19sq84ahdx3m7c2p2pxjcznmv6hys"))))
+                "0w632262dqzcnvq9s6jvc7naz93dayx51fsv05s0zb6cjwygbqjr"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
@@ -1295,18 +1511,19 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-bluster
   (package
    (name "r-bluster")
-   (version "1.0.0")
+   (version "1.2.1")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "bluster" version))
             (sha256
              (base32
-              "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61"))))
+              "128zd5vwlhmrkq0bpp1dxnkrcqfz1mjmdjlla4wqbjv7v6yyn6lg"))))
    (properties `((upstream-name . "bluster")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biocneighbors" ,r-biocneighbors)
       ("r-biocparallel" ,r-biocparallel)
+      ("r-cluster" ,r-cluster)
       ("r-igraph" ,r-igraph)
       ("r-matrix" ,r-matrix)
       ("r-rcpp" ,r-rcpp)
@@ -1324,13 +1541,13 @@ and evaluate clustering results.")
 (define-public r-ideoviz
   (package
     (name "r-ideoviz")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IdeoViz" version))
               (sha256
                (base32
-                "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
+                "17sx0v5lq2zmg098ps4ksj1h0yla3vlh6s2w1ahqsq0nvm193scm"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -1348,13 +1565,13 @@ arbitrary genomic intervals along chromosomal ideogram.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.24.1")
+    (version "2.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52"))))
+                "0dzj8wqbjzilh2dsaj3ylx958xqrv0c688ayfq2r1z7rs75qy7kx"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -1406,18 +1623,20 @@ absolute GSEA.")
 (define-public r-bisquerna
   (package
    (name "r-bisquerna")
-   (version "1.0.4")
+   (version "1.0.5")
    (source (origin
             (method url-fetch)
             (uri (cran-uri "BisqueRNA" version))
             (sha256
              (base32
-              "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
+              "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
    (properties `((upstream-name . "BisqueRNA")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-limsolve" ,r-limsolve)))
+   (native-inputs
+     `(("r-knitr" ,r-knitr)))
    (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
    (synopsis "Decomposition of bulk expression with single-cell sequencing")
    (description "This package provides tools to accurately estimate cell type
@@ -1501,17 +1720,45 @@ optimized in C++, and the main interface function provides an easy way of
 performing parallel computations on multicore machines.")
     (license license:gpl2+)))
 
+(define-public r-affy
+  (package
+    (name "r-affy")
+    (version "1.70.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affy" version))
+       (sha256
+        (base32
+         "0vz5y92gqcm0qk57qlba85bk683lzdr7vkmxv109rq6i17vdkkrm"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affyio" ,r-affyio)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-preprocesscore" ,r-preprocesscore)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://bioconductor.org/packages/affy")
+    (synopsis "Methods for affymetrix oligonucleotide arrays")
+    (description
+     "This package contains functions for exploratory oligonucleotide array
+analysis.")
+    (license license:lgpl2.0+)))
+
 (define-public r-affycomp
   (package
     (name "r-affycomp")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycomp" version))
        (sha256
         (base32
-         "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
+         "07my5scdh6h0y1bx1h9y5m4fa8bnmw389f83gkb7cf19w4vp36b2"))))
     (properties `((upstream-name . "affycomp")))
     (build-system r-build-system)
     (propagated-inputs `(("r-biobase" ,r-biobase)))
@@ -1525,14 +1772,14 @@ measures for Affymetrix Oligonucleotide Arrays.")
 (define-public r-affycompatible
   (package
     (name "r-affycompatible")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AffyCompatible" version))
        (sha256
         (base32
-         "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
+         "1xwz22wf2smsvmd0d5lfadbsgscnl3fl9msypy2mml38k048p6vj"))))
     (properties
      `((upstream-name . "AffyCompatible")))
     (build-system r-build-system)
@@ -1553,14 +1800,14 @@ Command Console} (AGCC)-compatible sample annotation files.")
 (define-public r-affycontam
   (package
     (name "r-affycontam")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyContam" version))
        (sha256
         (base32
-         "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
+         "0242ga68wrdk1kcmxfdbq73a0d3zhrzdlzkzphfg3q0zjbvg49jj"))))
     (properties `((upstream-name . "affyContam")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1578,14 +1825,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
 (define-public r-affycoretools
   (package
     (name "r-affycoretools")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycoretools" version))
        (sha256
         (base32
-         "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
+         "1dx861spr3kn1dxwhf43s5l1r7bmrq0h6538l3q64iiwzzc6krdh"))))
     (properties `((upstream-name . "affycoretools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1617,17 +1864,41 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
 to streamline the more common analyses that a Biostatistician might see.")
     (license license:artistic2.0)))
 
+(define-public r-affyio
+  (package
+    (name "r-affyio")
+    (version "1.62.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affyio" version))
+       (sha256
+        (base32
+         "07kibqsm888g06qqqa4648ph877kriy74kprbri8nyx83y8aspjr"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-zlibbioc" ,r-zlibbioc)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://github.com/bmbolstad/affyio")
+    (synopsis "Tools for parsing Affymetrix data files")
+    (description
+     "This package provides routines for parsing Affymetrix data files based
+upon file format information.  The primary focus is on accessing the CEL and
+CDF file formats.")
+    (license license:lgpl2.0+)))
+
 (define-public r-affxparser
   (package
     (name "r-affxparser")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affxparser" version))
        (sha256
         (base32
-         "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
+         "0n3yyrglzqzw0wqxl9igqvkj8qslw6yjkym3vcq0c93kkg7vk01l"))))
     (properties `((upstream-name . "affxparser")))
     (build-system r-build-system)
     (home-page "https://github.com/HenrikBengtsson/affxparser")
@@ -1648,14 +1919,14 @@ structure.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
+         "13ny596wh65sw7dbw0zd4h84d6k1w99g91c4sqy83mdzgpv73sz7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -1675,13 +1946,13 @@ microarrays.")
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.52.0")
+    (version "1.54.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
+                "117zh7iqa6phsrxrkv45kxraamm3vbfz5i1a8vkhyalhdbs5ssph"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
@@ -1689,6 +1960,7 @@ microarrays.")
      `(("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-dbi" ,r-dbi)
+       ("r-keggrest" ,r-keggrest)
        ("r-iranges" ,r-iranges)
        ("r-rsqlite" ,r-rsqlite)
        ("r-s4vectors" ,r-s4vectors)))
@@ -1701,17 +1973,43 @@ microarrays.")
 annotation data packages using SQLite data storage.")
     (license license:artistic2.0)))
 
+(define-public r-annotationfilter
+  (package
+    (name "r-annotationfilter")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AnnotationFilter" version))
+              (sha256
+               (base32
+                "0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa"))))
+    (properties
+     `((upstream-name . "AnnotationFilter")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomicranges" ,r-genomicranges)
+       ("r-lazyeval" ,r-lazyeval)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/Bioconductor/AnnotationFilter")
+    (synopsis "Facilities for filtering Bioconductor annotation resources")
+    (description
+     "This package provides classes and other infrastructure to implement
+filters for manipulating Bioconductor annotation resources.  The filters are
+used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
+    (license license:artistic2.0)))
+
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
+         "1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -1733,16 +2031,114 @@ annotation data packages using SQLite data storage.")
 databases.  Packages produced are intended to be used with AnnotationDbi.")
     (license license:artistic2.0)))
 
+(define-public r-annotationhub
+  (package
+    (name "r-annotationhub")
+    (version "3.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "AnnotationHub" version))
+       (sha256
+        (base32
+         "1p9773fv7j7q4x1sjqqaw32qy9lqn2gf6gkynh1d8n1kd7v7sclp"))))
+    (properties `((upstream-name . "AnnotationHub")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocfilecache" ,r-biocfilecache)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-biocversion" ,r-biocversion)
+       ("r-curl" ,r-curl)
+       ("r-dplyr" ,r-dplyr)
+       ("r-httr" ,r-httr)
+       ("r-interactivedisplaybase" ,r-interactivedisplaybase)
+       ("r-rappdirs" ,r-rappdirs)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-yaml" ,r-yaml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/AnnotationHub")
+    (synopsis "Client to access AnnotationHub resources")
+    (description
+     "This package provides a client for the Bioconductor AnnotationHub web
+resource.  The AnnotationHub web resource provides a central location where
+genomic files (e.g. VCF, bed, wig) and other resources from standard
+locations (e.g. UCSC, Ensembl) can be discovered.  The resource includes
+metadata about each resource, e.g., a textual description, tags, and date of
+modification.  The client creates and manages a local cache of files retrieved
+by the user, helping with quick and reproducible access.")
+    (license license:artistic2.0)))
+
+(define-public r-aroma-light
+  (package
+    (name "r-aroma-light")
+    (version "3.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "aroma.light" version))
+       (sha256
+        (base32
+         "1yvq6l1p8cpijvlib4fn9y88ihn0gaalrmgx82jgrfmnszkqn3y5"))))
+    (properties `((upstream-name . "aroma.light")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrixstats" ,r-matrixstats)
+       ("r-r-methodss3" ,r-r-methodss3)
+       ("r-r-oo" ,r-r-oo)
+       ("r-r-utils" ,r-r-utils)))
+    (home-page "https://github.com/HenrikBengtsson/aroma.light")
+    (synopsis "Methods for normalization and visualization of microarray data")
+    (description
+     "This package provides methods for microarray analysis that take basic
+data types such as matrices and lists of vectors.  These methods can be used
+standalone, be utilized in other packages, or be wrapped up in higher-level
+classes.")
+    (license license:gpl2+)))
+
+(define-public r-bamsignals
+  (package
+    (name "r-bamsignals")
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "bamsignals" version))
+       (sha256
+        (base32
+         "1ljrip0jlxjcljqac7vzvwqbcqil5v4f4s4bhpq4akvdkshas6mn"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/bamsignals")
+    (synopsis "Extract read count signals from bam files")
+    (description
+     "This package efficiently obtains count vectors from indexed bam
+files.  It counts the number of nucleotide sequence reads in given genomic
+ranges and it computes reads profiles and coverage profiles.  It also handles
+paired-end data.")
+    (license license:gpl2+)))
+
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.50.0")
+    (version "2.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
+                "1sg8w8860zhlz9s1pf75xa8asd2hyqsj13fh5xc37hf5yqdfkavr"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
@@ -1758,26 +2154,25 @@ on Bioconductor or which replace R functions.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.46.3")
+    (version "2.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
+                "1h8lzd63qvy1y75nlnhazpkyhl6g1hz80baqg20gpxbv38wkyf55"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biocfilecache" ,r-biocfilecache)
+       ("r-digest" ,r-digest)
        ("r-httr" ,r-httr)
-       ("r-openssl" ,r-openssl)
        ("r-progress" ,r-progress)
        ("r-rappdirs" ,r-rappdirs)
        ("r-stringr" ,r-stringr)
-       ("r-xml" ,r-xml)
-       ("r-xml2" ,r-xml2)))
+       ("r-xml" ,r-xml)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/biomaRt")
@@ -1796,13 +2191,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.24.1")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
+                "17w4gdajxxmsfgiwycp1d7rbxdqhc5jnngcb58ky0fv5xbv9f4j0"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -1851,19 +2246,20 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.58.0")
+    (version "2.60.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
+                "0xidh6wp0l47g1j9x8d4fs91ky6pi5nzf85ry801gqd2gqajh2zy"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-crayon" ,r-crayon)
+       ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-iranges" ,r-iranges)
        ("r-s4vectors" ,r-s4vectors)
        ("r-xvector" ,r-xvector)))
@@ -1875,17 +2271,90 @@ matching algorithms, and other utilities, for fast manipulation of large
 biological sequences or sets of sequences.")
     (license license:artistic2.0)))
 
+(define-public r-biovizbase
+  (package
+    (name "r-biovizbase")
+    (version "1.40.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "biovizBase" version))
+       (sha256
+        (base32
+         "14jyyg3ggdhaqhp0j4qf6dapykh76fygbaa4lr7czqbc5mr0iw23"))))
+    (properties `((upstream-name . "biovizBase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationfilter" ,r-annotationfilter)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-dichromat" ,r-dichromat)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-hmisc" ,r-hmisc)
+       ("r-iranges" ,r-iranges)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rlang" ,r-rlang)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "https://bioconductor.org/packages/biovizBase")
+    (synopsis "Basic graphic utilities for visualization of genomic data")
+    (description
+     "The biovizBase package is designed to provide a set of utilities, color
+schemes and conventions for genomic data.  It serves as the base for various
+high-level packages for biological data visualization.  This saves development
+effort and encourages consistency.")
+    (license license:artistic2.0)))
+
+(define-public r-bsgenome
+  (package
+    (name "r-bsgenome")
+    (version "1.60.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BSgenome" version))
+              (sha256
+               (base32
+                "1jhissp9ad1rn2p0bzr3yslbn84yqbaqgnn5p9hyacwr7mr091cn"))))
+    (properties
+     `((upstream-name . "BSgenome")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/BSgenome")
+    (synopsis "Infrastructure for Biostrings-based genome data packages")
+    (description
+     "This package provides infrastructure shared by all Biostrings-based
+genome data packages and support for efficient SNP representation.")
+    (license license:artistic2.0)))
+
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.56.0")
+    (version "2.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
+         "0f76pb7h8qc51mca5pq00m9p02sbkcj6ywfzli20qai2ykpfr71x"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1906,17 +2375,201 @@ biological sequences or sets of sequences.")
 analysis.")
     (license license:artistic2.0)))
 
+(define-public r-chipseeker
+  (package
+    (name "r-chipseeker")
+    (version "1.28.3")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ChIPseeker" version))
+              (sha256
+               (base32
+                "18hdgml80770c0xgd06zrl8px1ql9fa65rirfkq07z7rzpnd23rw"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-boot" ,r-boot)
+       ("r-enrichplot" ,r-enrichplot)
+       ("r-iranges" ,r-iranges)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gplots" ,r-gplots)
+       ("r-gtools" ,r-gtools)
+       ("r-dplyr" ,r-dplyr)
+       ("r-plotrix" ,r-plotrix)
+       ("r-dplyr" ,r-dplyr)
+       ("r-magrittr" ,r-magrittr)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-txdb-hsapiens-ucsc-hg19-knowngene"
+        ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
+    (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
+    (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
+    (description "This package implements functions to retrieve the nearest
+genes around the peak, annotate genomic region of the peak, statstical methods
+for estimate the significance of overlap among ChIP peak data sets, and
+incorporate GEO database for user to compare the own dataset with those
+deposited in database.  The comparison can be used to infer cooperative
+regulation and thus can be used to generate hypotheses.  Several visualization
+functions are implemented to summarize the coverage of the peak experiment,
+average profile and heatmap of peaks binding to TSS regions, genomic
+annotation, distance to TSS, and overlap of peaks or genes.")
+    (license license:artistic2.0)))
+
+(define-public r-chipseq
+  (package
+    (name "r-chipseq")
+    (version "1.42.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "chipseq" version))
+       (sha256
+        (base32
+         "078p9h0zghlhpd6cr54nww1mk7q97imx8yqfayw5m2yq4097ivbi"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shortread" ,r-shortread)))
+    (home-page "https://bioconductor.org/packages/chipseq")
+    (synopsis "Package for analyzing ChIPseq data")
+    (description
+     "This package provides tools for processing short read data from ChIPseq
+experiments.")
+    (license license:artistic2.0)))
+
+(define-public r-complexheatmap
+  (package
+    (name "r-complexheatmap")
+    (version "2.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ComplexHeatmap" version))
+       (sha256
+        (base32
+         "0jl96msj1njdrvngg68s50vmphvhi2lfwlv34x07pcdzgkjjs41f"))))
+    (properties
+     `((upstream-name . "ComplexHeatmap")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cairo" ,r-cairo)
+       ("r-circlize" ,r-circlize)
+       ("r-clue" ,r-clue)
+       ("r-colorspace" ,r-colorspace)
+       ("r-digest" ,r-digest)
+       ("r-doparallel" ,r-doparallel)
+       ("r-foreach" ,r-foreach)
+       ("r-getoptlong" ,r-getoptlong)
+       ("r-globaloptions" ,r-globaloptions)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-png" ,r-png)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page
+     "https://github.com/jokergoo/ComplexHeatmap")
+    (synopsis "Making Complex Heatmaps")
+    (description
+     "Complex heatmaps are efficient to visualize associations between
+different sources of data sets and reveal potential structures.  This package
+provides a highly flexible way to arrange multiple heatmaps and supports
+self-defined annotation graphics.")
+    (license license:gpl2+)))
+
+(define-public r-copywriter
+  (package
+    (name "r-copywriter")
+    (version "2.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "CopywriteR" version))
+       (sha256
+        (base32
+         "0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp"))))
+    (properties `((upstream-name . "CopywriteR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-chipseq" ,r-chipseq)
+       ("r-copyhelper" ,r-copyhelper)
+       ("r-data-table" ,r-data-table)
+       ("r-dnacopy" ,r-dnacopy)
+       ("r-futile-logger" ,r-futile-logger)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-gtools" ,r-gtools)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://github.com/PeeperLab/CopywriteR")
+    (synopsis "Copy number information from targeted sequencing")
+    (description
+     "CopywriteR extracts DNA copy number information from targeted sequencing
+by utilizing off-target reads.  It allows for extracting uniformly distributed
+copy number information, can be used without reference, and can be applied to
+sequencing data obtained from various techniques including chromatin
+immunoprecipitation and target enrichment on small gene panels.  Thereby,
+CopywriteR constitutes a widely applicable alternative to available copy
+number detection tools.")
+    (license license:gpl2)))
+
+(define-public r-deseq
+  (package
+    (name "r-deseq")
+    (version "1.39.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DESeq" version))
+       (sha256
+        (base32
+         "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
+    (properties `((upstream-name . "DESeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-genefilter" ,r-genefilter)
+       ("r-geneplotter" ,r-geneplotter)
+       ("r-lattice" ,r-lattice)
+       ("r-locfit" ,r-locfit)
+       ("r-mass" ,r-mass)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+    (home-page "https://www-huber.embl.de/users/anders/DESeq/")
+    (synopsis "Differential gene expression analysis")
+    (description
+     "This package provides tools for estimating variance-mean dependence in
+count data from high-throughput genetic sequencing assays and for testing for
+differential expression based on a model using the negative binomial
+distribution.")
+    (license license:gpl3+)))
+
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.30.1")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19"))))
+         "0r1brwmj7av0bj72jajn27vx3zs1bgg8qfbhf02fln6kf7im4kaz"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1947,14 +2600,14 @@ distribution.")
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
+         "1zywh30f4j4rj0f9w6yk5xr9mvdbg8gicy3wsb8yxdnamadyr7x4"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1989,16 +2642,85 @@ testing.  The package also provides functions for the visualization and
 exploration of the results.")
     (license license:gpl3+)))
 
+(define-public r-dirichletmultinomial
+  (package
+    (name "r-dirichletmultinomial")
+    (version "1.34.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DirichletMultinomial" version))
+       (sha256
+        (base32
+         "0ikmj0300lfzj6q1vyahfyx5kwi5h59mds7ym4f2j1bbxqzy6ssl"))))
+    (properties
+     `((upstream-name . "DirichletMultinomial")))
+    (build-system r-build-system)
+    (inputs
+     `(("gsl" ,gsl)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/DirichletMultinomial")
+    (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
+    (description
+     "Dirichlet-multinomial mixture models can be used to describe variability
+in microbial metagenomic data.  This package is an interface to code
+originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
+1-15.")
+    (license license:lgpl3)))
+
+(define-public r-edaseq
+  (package
+    (name "r-edaseq")
+    (version "2.26.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "EDASeq" version))
+       (sha256
+        (base32
+         "1mqpi2iz4azr31b3ajsqb4n9izjh85dx642844n059c8s2pfmivh"))))
+    (properties `((upstream-name . "EDASeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-aroma-light" ,r-aroma-light)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-biomart" ,r-biomart)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-shortread" ,r-shortread)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/drisso/EDASeq")
+    (synopsis "Exploratory data analysis and normalization for RNA-Seq")
+    (description
+     "This package provides support for numerical and graphical summaries of
+RNA-Seq genomic read data.  Provided within-lane normalization procedures to
+adjust for GC-content effect (or other gene-level effects) on read counts:
+loess robust local regression, global-scaling, and full-quantile
+normalization.  Between-lane normalization procedures to adjust for
+distributional differences between lanes (e.g., sequencing depth):
+global-scaling and full-quantile normalization.")
+    (license license:artistic2.0)))
+
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.32.1")
+    (version "3.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
+                "1ikl9y6hj2p92nrb1ydxy2410b3wrax83rfy2imaj0vgfmhsgx6g"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2017,17 +2739,123 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and
 CAGE.")
     (license license:gpl2+)))
 
+(define-public r-ensembldb
+  (package
+    (name "r-ensembldb")
+    (version "2.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ensembldb" version))
+       (sha256
+        (base32
+         "100m2mzxl4pmldqixzfdznnd4nqbykk2l7n4xazqjpnlpcldy2dj"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationfilter" ,r-annotationfilter)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-curl" ,r-curl)
+       ("r-dbi" ,r-dbi)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/jotsetung/ensembldb")
+    (synopsis "Utilities to create and use Ensembl-based annotation databases")
+    (description
+     "The package provides functions to create and use transcript-centric
+annotation databases/packages.  The annotation for the databases are directly
+fetched from Ensembl using their Perl API.  The functionality and data is
+similar to that of the TxDb packages from the @code{GenomicFeatures} package,
+but, in addition to retrieve all gene/transcript models and annotations from
+the database, the @code{ensembldb} package also provides a filter framework
+allowing to retrieve annotations for specific entries like genes encoded on a
+chromosome region or transcript models of lincRNA genes.")
+    ;; No version specified
+    (license license:lgpl3+)))
+
+(define-public r-fastseg
+  (package
+    (name "r-fastseg")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "fastseg" version))
+       (sha256
+        (base32
+         "006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
+    (synopsis "Fast segmentation algorithm for genetic sequencing data")
+    (description
+     "Fastseg implements a very fast and efficient segmentation algorithm.
+It can segment data from DNA microarrays and data from next generation
+sequencing for example to detect copy number segments.  Further it can segment
+data from RNA microarrays like tiling arrays to identify transcripts.  Most
+generally, it can segment data given as a matrix or as a vector.  Various data
+formats can be used as input to fastseg like expression set objects for
+microarrays or GRanges for sequencing data.")
+    (license license:lgpl2.0+)))
+
+(define-public r-gage
+  (package
+    (name "r-gage")
+    (version "2.42.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gage" version))
+       (sha256
+        (base32
+         "0z7hrwdm6my6p7z04bcpfhqk72pd0s1bdzvsiiym59qj79fbvb83"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-go-db" ,r-go-db)
+       ("r-graph" ,r-graph)
+       ("r-keggrest" ,r-keggrest)))
+    (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
+                              "articles/10.1186/1471-2105-10-161"))
+    (synopsis "Generally applicable gene-set enrichment for pathway analysis")
+    (description
+     "GAGE is a published method for gene set (enrichment or GSEA) or pathway
+analysis.  GAGE is generally applicable independent of microarray or RNA-Seq
+data attributes including sample sizes, experimental designs, assay platforms,
+and other types of heterogeneity.  The gage package provides functions for
+basic GAGE analysis, result processing and presentation.  In addition, it
+provides demo microarray data and commonly used gene set data based on KEGG
+pathways and GO terms.  These functions and data are also useful for gene set
+analysis using other methods.")
+    (license license:gpl2+)))
+
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.72.1")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
+         "0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)
@@ -2045,16 +2873,83 @@ CAGE.")
 high-throughput sequencing experiments.")
     (license license:artistic2.0)))
 
+(define-public r-geneoverlap
+  (package
+    (name "r-geneoverlap")
+    (version "1.28.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GeneOverlap" version))
+              (sha256
+               (base32
+                "1kfw3h68rvbafhklds6sfmviwv91nms8wk0ywzkjg5h3mmgxbsv9"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-gplots" ,r-gplots)))
+    (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
+    (synopsis "Test and visualize gene overlaps")
+    (description "This package can be used to test two sets of gene lists
+and visualize the results.")
+    (license license:gpl3)))
+
+(define-public r-genomation
+  (package
+    (name "r-genomation")
+    (version "1.24.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "genomation" version))
+              (sha256
+               (base32
+                "0qa3b4mfd7l1sy4pw64zr2d90y5apah900krxjl4x39acygg0i2r"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-data-table" ,r-data-table)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridbase" ,r-gridbase)
+       ("r-impute" ,r-impute)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-plotrix" ,r-plotrix)
+       ("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)
+       ("r-readr" ,r-readr)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-seqpattern" ,r-seqpattern)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+    (synopsis "Summary, annotation and visualization of genomic data")
+    (description
+     "This package provides a package for summary and annotation of genomic
+intervals.  Users can visualize and quantify genomic intervals over
+pre-defined functional regions, such as promoters, exons, introns, etc.  The
+genomic intervals represent regions with a defined chromosome position, which
+may be associated with a score, such as aligned reads from HT-seq experiments,
+TF binding sites, methylation scores, etc.  The package can use any tabular
+genomic feature data as long as it has minimal information on the locations of
+genomic intervals.  In addition, it can use BAM or BigWig files as input.")
+    (license license:artistic2.0)))
+
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.26.7")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "0fp7sp3jmc2a1hk4r624lfavx8gc2ik3lv43ksc2jmspg6cvh516"))))
+                "0wjd7sh7kr9lfcdbzm5jdynl84nfsl7nqvly92qqrdcxd2sjfr63"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -2075,16 +2970,127 @@ translation between different chromosome sequence naming conventions (e.g.,
 names in their natural, rather than lexicographic, order.")
     (license license:artistic2.0)))
 
+(define-public r-genomicalignments
+  (package
+    (name "r-genomicalignments")
+    (version "1.28.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomicAlignments" version))
+              (sha256
+               (base32
+                "00rq110jkh89nxgk05zh8kssxk8mb4dq0wjg3n7ivfmmm9wdwhp2"))))
+    (properties
+     `((upstream-name . "GenomicAlignments")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/GenomicAlignments")
+    (synopsis "Representation and manipulation of short genomic alignments")
+    (description
+     "This package provides efficient containers for storing and manipulating
+short genomic alignments (typically obtained by aligning short reads to a
+reference genome).  This includes read counting, computing the coverage,
+junction detection, and working with the nucleotide content of the
+alignments.")
+    (license license:artistic2.0)))
+
+(define-public r-genomicfeatures
+  (package
+    (name "r-genomicfeatures")
+    (version "1.44.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomicFeatures" version))
+              (sha256
+               (base32
+                "0y7lnvfcfrs72xbkn67xcqyz9csl5696mr2zl425fkhmnmimm4fg"))))
+    (properties
+     `((upstream-name . "GenomicFeatures")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocio" ,r-biocio)
+       ("r-biomart" ,r-biomart)
+       ("r-biostrings" ,r-biostrings)
+       ("r-dbi" ,r-dbi)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rcurl" ,r-rcurl)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/GenomicFeatures")
+    (synopsis "Tools for working with transcript centric annotations")
+    (description
+     "This package provides a set of tools and methods for making and
+manipulating transcript centric annotations.  With these tools the user can
+easily download the genomic locations of the transcripts, exons and cds of a
+given organism, from either the UCSC Genome Browser or a BioMart
+database (more sources will be supported in the future).  This information is
+then stored in a local database that keeps track of the relationship between
+transcripts, exons, cds and genes.  Flexible methods are provided for
+extracting the desired features in a convenient format.")
+    (license license:artistic2.0)))
+
+(define-public r-genomicfiles
+  (package
+    (name "r-genomicfiles")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "GenomicFiles" version))
+       (sha256
+        (base32
+         "1plh14m7w6calw5yxcxp7g4bg8q00ax85m517wap78bni975k13y"))))
+    (properties `((upstream-name . "GenomicFiles")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixgenerics" ,r-matrixgenerics)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "https://bioconductor.org/packages/GenomicFiles")
+    (synopsis "Distributed computing by file or by range")
+    (description
+     "This package provides infrastructure for parallel computations
+distributed by file or by range.  User defined mapper and reducer functions
+provide added flexibility for data combination and manipulation.")
+    (license license:artistic2.0)))
+
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.42.0")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
+                "1qxc6dcwdlkan3hg0j9yfhz7gyi9qg671yj6zizsk6mzl7qqva0x"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -2109,14 +3115,14 @@ manipulating genomic intervals and variables defined along a genome.")
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.56.0")
+    (version "2.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
+         "0jjswy6qmfgr2f6vk3y9pdvs9x91gn31h55qllgh0qb2cb26g9wa"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2140,14 +3146,14 @@ testing and other simple calculations.")
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.52.1")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
+         "0946kkykms79mqnx262q20xzrrhv7cv723xh378335ff41qyf63n"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2169,14 +3175,14 @@ Enrichment Analysis} (GSEA).")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.32.1")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
+         "0q5pp04rq2gsh1kibvp8bvjkqc1kb46qpnj6agqp2vyqhrrfrm99"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -2186,16 +3192,120 @@ Enrichment Analysis} (GSEA).")
 the Human Protein Atlas project.")
     (license license:artistic2.0)))
 
+(define-public r-rhtslib
+  (package
+    (name "r-rhtslib")
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rhtslib" version))
+       (sha256
+        (base32
+         "0acpgv98529ic2i2k03knz05akb6h51wbz7sr5zgi8gk4nmawrlf"))))
+    (properties `((upstream-name . "Rhtslib")))
+    (build-system r-build-system)
+    ;; Without this a temporary directory ends up in the Rhtslib.so binary,
+    ;; which makes R abort the build.
+    (arguments '(#:configure-flags '("--no-staged-install")))
+    (propagated-inputs
+     `(("curl" ,curl)
+       ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/nhayden/Rhtslib")
+    (synopsis "High-throughput sequencing library as an R package")
+    (description
+     "This package provides the HTSlib C library for high-throughput
+nucleotide sequence analysis.  The package is primarily useful to developers
+of other R packages who wish to make use of HTSlib.")
+    (license license:lgpl2.0+)))
+
+(define-public r-impute
+  (package
+    (name "r-impute")
+    (version "1.66.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "impute" version))
+              (sha256
+               (base32
+                "0pprkv25avxhllddcssvqvy3nibmqkfwaq4xnlhka7858gyiyd1k"))))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/impute")
+    (synopsis "Imputation for microarray data")
+    (description
+     "This package provides a function to impute missing gene expression
+microarray data, using nearest neighbor averaging.")
+    (license license:gpl2+)))
+
+(define-public r-interactivedisplaybase
+  (package
+    (name "r-interactivedisplaybase")
+    (version "1.30.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "interactiveDisplayBase" version))
+       (sha256
+        (base32
+         "00rgrrmglslgb6j7whp0m5dlyl4436r647br05rrpv8cxrmbs2iv"))))
+    (properties
+     `((upstream-name . "interactiveDisplayBase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-dt" ,r-dt)
+       ("r-shiny" ,r-shiny)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
+    (synopsis "Base package for web displays of Bioconductor objects")
+    (description
+     "This package contains the basic methods needed to generate interactive
+Shiny-based display methods for Bioconductor objects.")
+    (license license:artistic2.0)))
+
+(define-public r-keggrest
+  (package
+    (name "r-keggrest")
+    (version "1.32.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "KEGGREST" version))
+       (sha256
+        (base32
+         "15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd"))))
+    (properties `((upstream-name . "KEGGREST")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-httr" ,r-httr)
+       ("r-png" ,r-png)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/KEGGREST")
+    (synopsis "Client-side REST access to KEGG")
+    (description
+     "This package provides a package that provides a client interface to the
+@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
+    (license license:artistic2.0)))
+
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.46.0")
+    (version "3.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
+                "1mkpl2b1ksylc6dih4a6kgjjia8advikzmqmv762j4r7gya950pf"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -2205,17 +3315,408 @@ and the assessment of differential expression.  The analysis methods apply to
 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
     (license license:gpl2+)))
 
+(define-public r-methylkit
+  (package
+    (name "r-methylkit")
+    (version "1.18.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "methylKit" version))
+              (sha256
+               (base32
+                "147nag4rz2xpjkkf8rmhja9k4ixjj1hsb0lq3lw7mw6q67zxsvf3"))))
+    (properties `((upstream-name . "methylKit")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-emdbook" ,r-emdbook)
+       ("r-fastseg" ,r-fastseg)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-gtools" ,r-gtools)
+       ("r-iranges" ,r-iranges)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-limma" ,r-limma)
+       ("r-mclust" ,r-mclust)
+       ("r-mgcv" ,r-mgcv)
+       ("r-qvalue" ,r-qvalue)
+       ("r-r-utils" ,r-r-utils)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
+    (home-page "https://github.com/al2na/methylKit")
+    (synopsis
+     "DNA methylation analysis from high-throughput bisulfite sequencing results")
+    (description
+     "MethylKit is an R package for DNA methylation analysis and annotation
+from high-throughput bisulfite sequencing.  The package is designed to deal
+with sequencing data from @dfn{Reduced representation bisulfite
+sequencing} (RRBS) and its variants, but also target-capture methods and whole
+genome bisulfite sequencing.  It also has functions to analyze base-pair
+resolution 5hmC data from experimental protocols such as oxBS-Seq and
+TAB-Seq.")
+    (license license:artistic2.0)))
+
+(define-public r-motifrg
+  (package
+    (name "r-motifrg")
+    (version "1.31.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "motifRG" version))
+       (sha256
+        (base32
+         "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
+    (properties `((upstream-name . "motifRG")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+       ("r-iranges" ,r-iranges)
+       ("r-seqlogo" ,r-seqlogo)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/motifRG")
+    (synopsis "Discover motifs in high throughput sequencing data")
+    (description
+     "This package provides tools for discriminative motif discovery in high
+throughput genetic sequencing data sets using regression methods.")
+    (license license:artistic2.0)))
+
+(define-public r-mutationalpatterns
+  (package
+    (name "r-mutationalpatterns")
+    (version "3.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MutationalPatterns" version))
+       (sha256
+        (base32
+         "0433i4xbz8hrfaj8fxgzps3x8dqrl5vgwzg7qmp4cy5sb1lw5wvs"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ;; These two packages are suggested packages
+       ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
+       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+       ("r-cowplot" ,r-cowplot)
+       ("r-dplyr" ,r-dplyr)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggalluvial" ,r-ggalluvial)
+       ("r-ggdendro" ,r-ggdendro)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iranges" ,r-iranges)
+       ("r-magrittr" ,r-magrittr)
+       ("r-nmf" ,r-nmf)
+       ("r-pracma" ,r-pracma)
+       ("r-purrr" ,r-purrr)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "https://bioconductor.org/packages/MutationalPatterns/")
+    (synopsis "Extract and visualize mutational patterns in genomic data")
+    (description "This package provides an extensive toolset for the
+characterization and visualization of a wide range of mutational patterns
+in SNV base substitution data.")
+    (license license:expat)))
+
+(define-public r-msnbase
+  (package
+    (name "r-msnbase")
+    (version "2.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MSnbase" version))
+       (sha256
+        (base32
+         "1z7s17j6zgb70m0khyf9icqlnbnzlivca7vw7j0vxyw417ld9lkr"))))
+    (properties `((upstream-name . "MSnbase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-digest" ,r-digest)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-impute" ,r-impute)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-maldiquant" ,r-maldiquant)
+       ("r-mass" ,r-mass)
+       ("r-mscoreutils" ,r-mscoreutils)
+       ("r-mzid" ,r-mzid)
+       ("r-mzr" ,r-mzr)
+       ("r-pcamethods" ,r-pcamethods)
+       ("r-plyr" ,r-plyr)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rcpp" ,r-rcpp)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
+       ("r-vsn" ,r-vsn)
+       ("r-xml" ,r-xml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/lgatto/MSnbase")
+    (synopsis "Base functions and classes for MS-based proteomics")
+    (description
+     "This package provides basic plotting, data manipulation and processing
+of mass spectrometry based proteomics data.")
+    (license license:artistic2.0)))
+
+(define-public r-msnid
+  (package
+    (name "r-msnid")
+    (version "1.26.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MSnID" version))
+       (sha256
+        (base32
+         "0r3vgigf4fk0xzfg8gcvad01jdh0fysh6x22m9qy77x6glyrxcj2"))))
+    (properties `((upstream-name . "MSnID")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-HOME
+           (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationhub" ,r-annotationhub)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocstyle" ,r-biocstyle)
+       ("r-biostrings" ,r-biostrings)
+       ("r-data-table" ,r-data-table)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dplyr" ,r-dplyr)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iterators" ,r-iterators)
+       ("r-msnbase" ,r-msnbase)
+       ("r-msmstests" ,r-msmstests)
+       ("r-mzid" ,r-mzid)
+       ("r-mzr" ,r-mzr)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-purrr" ,r-purrr)
+       ("r-r-cache" ,r-r-cache)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rlang" ,r-rlang)
+       ("r-runit" ,r-runit)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-xtable" ,r-xtable)))
+    (home-page "https://bioconductor.org/packages/MSnID")
+    (synopsis "Utilities for LC-MSn proteomics identifications")
+    (description
+     "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
+from mzIdentML (leveraging the mzID package) or text files.  After collating
+the search results from multiple datasets it assesses their identification
+quality and optimize filtering criteria to achieve the maximum number of
+identifications while not exceeding a specified false discovery rate.  It also
+contains a number of utilities to explore the MS/MS results and assess missed
+and irregular enzymatic cleavages, mass measurement accuracy, etc.")
+    (license license:artistic2.0)))
+
+(define-public r-mzid
+  (package
+    (name "r-mzid")
+    (version "1.30.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "mzID" version))
+       (sha256
+        (base32
+         "1wsy6frxa5602jqb1nlqv39mzgpid8wfyvb9m2jb6srv7p59rgys"))))
+    (properties `((upstream-name . "mzID")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-doparallel" ,r-doparallel)
+       ("r-foreach" ,r-foreach)
+       ("r-iterators" ,r-iterators)
+       ("r-plyr" ,r-plyr)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-xml" ,r-xml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/mzID")
+    (synopsis "Parser for mzIdentML files")
+    (description
+     "This package provides a parser for mzIdentML files implemented using the
+XML package.  The parser tries to be general and able to handle all types of
+mzIdentML files with the drawback of having less pretty output than a vendor
+specific parser.")
+    (license license:gpl2+)))
+
+(define-public r-mzr
+  (package
+    (name "r-mzr")
+    (version "2.26.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "mzR" version))
+       (sha256
+        (base32
+         "1m5xvnv0rxyrfri4jwyyryr13d55nyhqvfc5xxg5mpskw2v029kp"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (delete-file-recursively "src/boost")
+           #t))))
+    (properties `((upstream-name . "mzR")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-boost
+           (lambda _
+             (substitute* "src/Makevars"
+               (("\\./boost/libs.*") "")
+               (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
+               (("\\ARCH_OBJS=" line)
+                (string-append line
+                               "\nBOOST_LIBS=-lboost_system -lboost_regex \
+-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
+             #t)))))
+    (inputs
+     `(;; Our default boost package won't work here, unfortunately, even with
+       ;; mzR version 2.26.0.
+       ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-ncdf4" ,r-ncdf4)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/sneumann/mzR/")
+    (synopsis "Parser for mass spectrometry data files")
+    (description
+     "The mzR package provides a unified API to the common file formats and
+parsers available for mass spectrometry data.  It comes with a wrapper for the
+ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
+The package contains the original code written by the ISB, and a subset of the
+proteowizard library for mzML and mzIdentML.  The netCDF reading code has
+previously been used in XCMS.")
+    (license license:artistic2.0)))
+
+(define-public r-organismdbi
+  (package
+    (name "r-organismdbi")
+    (version "1.34.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "OrganismDbi" version))
+       (sha256
+        (base32
+         "0p8ccpdchdwci4kv9y07wdadzgms8nipvg6rm1rll35jcflnnkxi"))))
+    (properties `((upstream-name . "OrganismDbi")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-dbi" ,r-dbi)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-graph" ,r-graph)
+       ("r-iranges" ,r-iranges)
+       ("r-rbgl" ,r-rbgl)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/OrganismDbi")
+    (synopsis "Software to enable the smooth interfacing of database packages")
+    (description "The package enables a simple unified interface to several
+annotation packages each of which has its own schema by taking advantage of
+the fact that each of these packages implements a select methods.")
+    (license license:artistic2.0)))
+
+(define-public r-pcamethods
+  (package
+    (name "r-pcamethods")
+    (version "1.84.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "pcaMethods" version))
+       (sha256
+        (base32
+         "1ccqsxn487dy92c2d1iffh9917z4zq5ia92zv2h6pi00jjc6ymb5"))))
+    (properties `((upstream-name . "pcaMethods")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-mass" ,r-mass)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/hredestig/pcamethods")
+    (synopsis "Collection of PCA methods")
+    (description
+     "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
+Inverse Non-Linear PCA and the conventional SVD PCA.  A cluster based method
+for missing value estimation is included for comparison.  BPCA, PPCA and
+NipalsPCA may be used to perform PCA on incomplete data as well as for
+accurate missing value estimation.  A set of methods for printing and plotting
+the results is also provided.  All PCA methods make use of the same data
+structure (pcaRes) to provide a common interface to the PCA results.")
+    (license license:gpl3+)))
+
+(define-public r-protgenerics
+  (package
+    (name "r-protgenerics")
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ProtGenerics" version))
+       (sha256
+        (base32
+         "1c79k8nc28782w5gxi7pkm8jmddq1hdw6khs9kgsp8dyk60ak6fq"))))
+    (properties `((upstream-name . "ProtGenerics")))
+    (build-system r-build-system)
+    (home-page "https://github.com/lgatto/ProtGenerics")
+    (synopsis "S4 generic functions for proteomics infrastructure")
+    (description
+     "This package provides S4 generic functions needed by Bioconductor
+proteomics packages.")
+    (license license:artistic2.0)))
+
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
+         "0l40ibf8g5s4ay83s92l198jjqc5l09hcmxqcjrpifvp5pjf9yy5"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2228,17 +3729,67 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 the graph algorithms contained in the Boost library.")
     (license license:artistic2.0)))
 
+(define-public r-rcas
+  (package
+    (name "r-rcas")
+    (version "1.18.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "RCAS" version))
+              (sha256
+               (base32
+                "0l92v870ndna8zjqwzf22fb9vyhkh6942v4gaiqr1yc4qr521p5p"))))
+    (properties `((upstream-name . "RCAS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+       ("r-cowplot" ,r-cowplot)
+       ("r-data-table" ,r-data-table)
+       ("r-dt" ,r-dt)
+       ("r-genomation" ,r-genomation)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggseqlogo" ,r-ggseqlogo)
+       ("r-gprofiler2" ,r-gprofiler2)
+       ("r-iranges" ,r-iranges)
+       ("r-knitr" ,r-knitr)
+       ("r-pbapply" ,r-pbapply)
+       ("r-pheatmap" ,r-pheatmap)
+       ("r-plotly" ,r-plotly)
+       ("r-plotrix" ,r-plotrix)
+       ("r-proxy" ,r-proxy)
+       ("r-ranger" ,r-ranger)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-s4vectors" ,r-s4vectors)
+       ("pandoc" ,pandoc)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (synopsis "RNA-centric annotation system")
+    (description
+     "RCAS aims to be a standalone RNA-centric annotation system that provides
+intuitive reports and publication-ready graphics.  This package provides the R
+library implementing most of the pipeline's features.")
+    (home-page "https://github.com/BIMSBbioinfo/RCAS")
+    (license license:artistic2.0)))
+
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
+         "0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2262,14 +3813,14 @@ region sets and other genomic features.")
 (define-public r-reportingtools
   (package
     (name "r-reportingtools")
-    (version "2.30.2")
+    (version "2.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReportingTools" version))
        (sha256
         (base32
-         "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb"))))
+         "0v6wzfswwcd1xdxgwa9gzlkmavr4p55jy11k84anh0rs0xx3dmmj"))))
     (properties
      `((upstream-name . "ReportingTools")))
     (build-system r-build-system)
@@ -2309,16 +3860,70 @@ reports together for a particular project that can be viewed in a web
 browser.")
     (license license:artistic2.0)))
 
+(define-public r-rhdf5
+  (package
+    (name "r-rhdf5")
+    (version "2.36.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "rhdf5" version))
+              (sha256
+               (base32
+                "1a5kw9ry9cr258al0x3q0ss5xn1ymscdypx51vzzgzamhy7dqakz"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rhdf5filters" ,r-rhdf5filters)
+       ("r-rhdf5lib" ,r-rhdf5lib)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/rhdf5")
+    (synopsis "HDF5 interface to R")
+    (description
+     "This R/Bioconductor package provides an interface between HDF5 and R.
+HDF5's main features are the ability to store and access very large and/or
+complex datasets and a wide variety of metadata on mass storage (disk) through
+a completely portable file format.  The rhdf5 package is thus suited for the
+exchange of large and/or complex datasets between R and other software
+package, and for letting R applications work on datasets that are larger than
+the available RAM.")
+    (license license:artistic2.0)))
+
+(define-public r-rhdf5filters
+  (package
+    (name "r-rhdf5filters")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "rhdf5filters" version))
+       (sha256
+        (base32
+         "133v0s452acspi4dbf6gsa2xrr0qza86jdjjbpwhdv6zfd1djbgc"))))
+    (properties `((upstream-name . "rhdf5filters")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rhdf5lib" ,r-rhdf5lib)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/grimbough/rhdf5filters")
+    (synopsis "HDF5 compression filters")
+    (description
+     "This package provides a collection of compression filters for use with
+HDF5 datasets.")
+    (license license:bsd-2)))
+
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.6.0")
+    (version "2.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
+                "0arhh5bbx3pmxmkh5sjgczcswqy83d35r7cjhd2knpczdvrixaq5"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -2330,8 +3935,7 @@ browser.")
              (substitute* "DESCRIPTION"
                (("zlibbioc, ") ""))
              (substitute* "NAMESPACE"
-               (("import\\(zlibbioc\\)") ""))
-             #t)))))
+               (("import\\(zlibbioc\\)") "")))))))
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biocparallel" ,r-biocparallel)
@@ -2352,17 +3956,173 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
 tab-delimited (tabix) files.")
     (license license:expat)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package:
+;; s4vectors.
+(define-public r-restfulr
+  (package
+    (name "r-restfulr")
+    (version "0.0.13")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "restfulr" version))
+       (sha256
+        (base32
+         "1dk45mzrr6ka92yjz7hfhkj12kpx1wg4szv1h1mg80mgga4ganbv"))))
+    (properties `((upstream-name . "restfulr")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcurl" ,r-rcurl)
+       ("r-rjson" ,r-rjson)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xml" ,r-xml)
+       ("r-yaml" ,r-yaml)))
+    (home-page "https://cran.r-project.org/package=restfulr")
+    (synopsis "R interface to RESTful web services")
+    (description
+     "This package models a RESTful service as if it were a nested R list.")
+    (license license:artistic2.0)))
+
+(define-public r-rtracklayer
+  (package
+    (name "r-rtracklayer")
+    (version "1.52.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "rtracklayer" version))
+              (sha256
+               (base32
+                "0iic0g0clsjd9ypdmfs6k52hrnmfszhxzg0xx89nszpasf69wghv"))))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-zlib
+           (lambda _
+             (substitute* "DESCRIPTION"
+               ((" zlibbioc,") ""))
+             (substitute* "NAMESPACE"
+               (("import\\(zlibbioc\\)") "")))))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocio" ,r-biocio)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rcurl" ,r-rcurl)
+       ("r-restfulr" ,r-restfulr)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xml" ,r-xml)
+       ("r-xvector" ,r-xvector)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (home-page "https://bioconductor.org/packages/rtracklayer")
+    (synopsis "R interface to genome browsers and their annotation tracks")
+    (description
+     "rtracklayer is an extensible framework for interacting with multiple
+genome browsers (currently UCSC built-in) and manipulating annotation tracks
+in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
+built-in).  The user may export/import tracks to/from the supported browsers,
+as well as query and modify the browser state, such as the current viewport.")
+    (license license:artistic2.0)))
+
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-samr
+  (package
+    (name "r-samr")
+    (version "3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "samr" version))
+       (sha256
+        (base32
+         "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
+    (properties `((upstream-name . "samr")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gsa" ,r-gsa)
+       ("r-impute" ,r-impute)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-openxlsx" ,r-openxlsx)
+       ("r-shiny" ,r-shiny)
+       ("r-shinyfiles" ,r-shinyfiles)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://statweb.stanford.edu/~tibs/SAM/")
+    (synopsis "Significance analysis of Microarrays")
+    (description
+     "This is a package for significance analysis of Microarrays for
+differential expression analysis, RNAseq data and related problems.")
+    ;; Any version of the LGPL
+    (license license:lgpl3+)))
+
+(define-public r-seqlogo
+  (package
+    (name "r-seqlogo")
+    (version "1.58.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "seqLogo" version))
+       (sha256
+        (base32
+         "1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp"))))
+    (properties `((upstream-name . "seqLogo")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/seqLogo")
+    (synopsis "Sequence logos for DNA sequence alignments")
+    (description
+     "seqLogo takes the position weight matrix of a DNA sequence motif and
+plots the corresponding sequence logo as introduced by Schneider and
+Stephens (1990).")
+    (license license:lgpl2.0+)))
+
+(define-public r-seqpattern
+  (package
+    (name "r-seqpattern")
+    (version "1.24.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "seqPattern" version))
+              (sha256
+               (base32
+                "0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay"))))
+    (properties
+     `((upstream-name . "seqPattern")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-plotrix" ,r-plotrix)))
+    (home-page "https://bioconductor.org/packages/seqPattern")
+    (synopsis "Visualising oligonucleotide patterns and motif occurrences")
+    (description
+     "This package provides tools to visualize oligonucleotide patterns and
+sequence motif occurrences across a large set of sequences centred at a common
+reference point and sorted by a user defined feature.")
+    (license license:gpl3+)))
+
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
+         "0zqinw3c6h5v1c5nhzkiziirws16nbviccgw8nj2d22r33dbqwp3"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -2395,16 +4155,111 @@ purposes.  The package also contains legacy support for early single-end,
 ungapped alignment formats.")
     (license license:artistic2.0)))
 
+(define-public r-trajectoryutils
+  (package
+    (name "r-trajectoryutils")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "TrajectoryUtils" version))
+       (sha256
+        (base32
+         "1b7mg3ypp1ay98cav47h9vn692lx0n9b5b0hpansgnkr5prb823b"))))
+    (properties
+     `((upstream-name . "TrajectoryUtils")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-igraph" ,r-igraph)
+       ("r-matrix" ,r-matrix)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/TrajectoryUtils")
+    (synopsis "Single-cell trajectory analysis utilities")
+    (description
+     "This package implements low-level utilities for single-cell trajectory
+analysis, primarily intended for re-use inside higher-level packages.  It
+includes a function to create a cluster-level minimum spanning tree and data
+structures to hold pseudotime inference results.")
+    (license license:gpl3)))
+
+(define-public r-slingshot
+  (package
+   (name "r-slingshot")
+   (version "2.0.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "slingshot" version))
+            (sha256
+             (base32
+              "1aqsz2kxwax8d8d5iv3zk5hlyk5aya1wbxs1wky2rgccw4d35whx"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-igraph" ,r-igraph)
+      ("r-matrixstats" ,r-matrixstats)
+      ("r-princurve" ,r-princurve)
+      ("r-s4vectors" ,r-s4vectors)
+      ("r-singlecellexperiment" ,r-singlecellexperiment)
+      ("r-summarizedexperiment" ,r-summarizedexperiment)
+      ("r-trajectoryutils" ,r-trajectoryutils)))
+   (native-inputs
+    `(("r-knitr" ,r-knitr)))
+   (home-page "https://bioconductor.org/packages/slingshot")
+   (synopsis "Tools for ordering single-cell sequencing")
+   (description "This package provides functions for inferring continuous,
+branching lineage structures in low-dimensional data.  Slingshot was designed
+to model developmental trajectories in single-cell RNA sequencing data and
+serve as a component in an analysis pipeline after dimensionality reduction
+and clustering.  It is flexible enough to handle arbitrarily many branching
+events and allows for the incorporation of prior knowledge through supervised
+graph construction.")
+   (license license:artistic2.0)))
+
+(define-public r-structuralvariantannotation
+  (package
+    (name "r-structuralvariantannotation")
+    (version "1.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "StructuralVariantAnnotation" version))
+       (sha256
+        (base32
+         "10h63h1v87nvm3bfyr6dsjlbmzxf1vks30d0xz6q4hssqq9xlzgv"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-assertthat" ,r-assertthat)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-dplyr" ,r-dplyr)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-rlang" ,r-rlang)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-stringr" ,r-stringr)
+       ("r-variantannotation" ,r-variantannotation)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
+    (synopsis "R package designed to simplify structural variant analysis")
+    (description
+     "This package contains useful helper functions for dealing with structural
+variants in VCF format.  The packages contains functions for parsing VCFs from
+a number of popular callers as well as functions for dealing with breakpoints
+involving two separate genomic loci encoded as GRanges objects.")
+    (license license:gpl3)))
+
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps"))))
+                "16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -2429,17 +4284,48 @@ typically represent genomic ranges of interest and the columns represent
 samples.")
     (license license:artistic2.0)))
 
+(define-public r-sva
+  (package
+    (name "r-sva")
+    (version "3.40.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "sva" version))
+       (sha256
+        (base32
+         "12jkcybdfspabh7x124d44l9fj1hwwg3gvcqxvz5wpkiflc2vkji"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-edger" ,r-edger)
+       ("r-genefilter" ,r-genefilter)
+       ("r-mgcv" ,r-mgcv)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-limma" ,r-limma)))
+    (home-page "https://bioconductor.org/packages/sva")
+    (synopsis "Surrogate variable analysis")
+    (description
+     "This package contains functions for removing batch effects and other
+unwanted variation in high-throughput experiment.  It also contains functions
+for identifying and building surrogate variables for high-dimensional data
+sets.  Surrogate variables are covariates constructed directly from
+high-dimensional data like gene expression/RNA sequencing/methylation/brain
+imaging data that can be used in subsequent analyses to adjust for unknown,
+unmodeled, or latent sources of noise.")
+    (license license:artistic2.0)))
+
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "1.24.6")
+    (version "1.26.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "05qnn105gm423fka4kb84vpgzjmz1py6mxpfa2agwwmc5v012qbp"))))
+         "1apqi5ih06s37v7wpp13ybksiinrwj0ii6mx6vvvfkb6ix0wljws"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2465,6 +4351,7 @@ samples.")
        ("r-shortread" ,r-shortread)
        ("r-stringr" ,r-stringr)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-testthat" ,r-testthat)
        ("r-yaml" ,r-yaml)
        ("r-variantannotation" ,r-variantannotation)))
     (native-inputs
@@ -2483,16 +4370,73 @@ experimental designs is facilitated by a consistently implemented sample
 annotation infrastructure.")
     (license license:artistic2.0)))
 
+(define-public r-topgo
+  (package
+    (name "r-topgo")
+    (version "2.44.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "topGO" version))
+              (sha256
+               (base32
+                "1ggi7yrhkyi85p3sfj3yd95n9mzq1xpff28ixa4dl9yzasks1v5a"))))
+    (properties
+     `((upstream-name . "topGO")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-dbi" ,r-dbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-go-db" ,r-go-db)
+       ("r-graph" ,r-graph)
+       ("r-lattice" ,r-lattice)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-sparsem" ,r-sparsem)))
+    (home-page "https://bioconductor.org/packages/topGO")
+    (synopsis "Enrichment analysis for gene ontology")
+    (description
+     "The topGO package provides tools for testing @dfn{gene ontology} (GO)
+terms while accounting for the topology of the GO graph.  Different test
+statistics and different methods for eliminating local similarities and
+dependencies between GO terms can be implemented and applied.")
+    ;; Any version of the LGPL applies.
+    (license license:lgpl2.1+)))
+
+(define-public r-tximport
+  (package
+    (name "r-tximport")
+    (version "1.20.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "tximport" version))
+              (sha256
+               (base32
+                "0ip2yr0zspf2aagskxl4dwncr48dw5qb90an3sswnnh2dqdb82if"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/tximport")
+    (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
+    (description
+     "This package provides tools to import transcript-level abundance,
+estimated counts and transcript lengths, and to summarize them into matrices
+for use with downstream gene-level analysis packages.  Average transcript
+length, weighted by sample-specific transcript abundance estimates, is
+provided as a matrix which can be used as an offset for different expression
+of gene-level counts.")
+    (license license:gpl2+)))
+
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.36.0")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
+                "0c9r00j8a3bs6n0dv4wi17jc1ljzvr3r2bi4h9axhcsf2ip906rh"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (propagated-inputs
@@ -2521,16 +4465,52 @@ annotation infrastructure.")
 coding changes and predict coding outcomes.")
     (license license:artistic2.0)))
 
+(define-public r-vsn
+  (package
+    (name "r-vsn")
+    (version "3.60.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "vsn" version))
+       (sha256
+        (base32
+         "0nppph3kv8z83368snb8s3n4vcqj829yyi1kh4q09qvq18rhvssv"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-biobase" ,r-biobase)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-lattice" ,r-lattice)
+       ("r-limma" ,r-limma)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
+    (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
+    (synopsis "Variance stabilization and calibration for microarray data")
+    (description
+     "The package implements a method for normalising microarray intensities,
+and works for single- and multiple-color arrays.  It can also be used for data
+from other technologies, as long as they have similar format.  The method uses
+a robust variant of the maximum-likelihood estimator for an
+additive-multiplicative error model and affine calibration.  The model
+incorporates data calibration step (a.k.a.  normalization), a model for the
+dependence of the variance on the mean intensity and a variance stabilizing
+data transformation.  Differences between transformed intensities are
+analogous to \"normalized log-ratios\".  However, in contrast to the latter,
+their variance is independent of the mean, and they are usually more sensitive
+and specific in detecting differential transcription.")
+    (license license:artistic2.0)))
+
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.30.0")
+    (version "0.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
+                "1cw34gd9iaspl0v737xl7rngq63zrj03a5ngai15ggrnv1sq2aqr"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
@@ -2557,17 +4537,36 @@ coding changes and predict coding outcomes.")
 \"externally\" (behind an R external pointer, or on disk).")
     (license license:artistic2.0)))
 
+(define-public r-zlibbioc
+  (package
+    (name "r-zlibbioc")
+    (version "1.38.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "zlibbioc" version))
+              (sha256
+               (base32
+                "1dv5bf12kzk1yzyfs3g5syim16sbi44kalvzj2i2xcnxnl6x60ip"))))
+    (properties
+     `((upstream-name . "zlibbioc")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/zlibbioc")
+    (synopsis "Provider for zlib-1.2.5 to R packages")
+    (description "This package uses the source code of zlib-1.2.5 to create
+libraries for systems that do not have these available via other means.")
+    (license license:artistic2.0)))
+
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
+         "1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)
@@ -2585,14 +4584,14 @@ coding changes and predict coding outcomes.")
 (define-public r-oligoclasses
   (package
     (name "r-oligoclasses")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligoClasses" version))
        (sha256
         (base32
-         "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
+         "1nsfyfpj264h6y322pzz0i001b0m862j3skbq5rjwlrj1p8j2gi7"))))
     (properties `((upstream-name . "oligoClasses")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2620,14 +4619,14 @@ packages.")
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.54.1")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
+         "0fyq77im6s79havjwbchhqhnllxs134jsi98g6msxz66h16lj3al"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -2656,14 +4655,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
+         "0xssanffh1hr7f48mnazcpwi25rdp7mxlyb9nbf4q2mp7m40jnpm"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -2711,13 +4710,13 @@ integration with @code{Rcpp}.")
 (define-public r-apeglm
   (package
    (name "r-apeglm")
-   (version "1.12.0")
+   (version "1.14.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "apeglm" version))
             (sha256
              (base32
-              "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
+              "1xld6ar440achik4dbd7vhiw6jfj0sb96jm52n7hav5bv4gag3mh"))))
    (properties `((upstream-name . "apeglm")))
    (build-system r-build-system)
    (propagated-inputs
@@ -2738,13 +4737,13 @@ posterior for individual coefficients.")
 (define-public r-greylistchip
   (package
    (name "r-greylistchip")
-   (version "1.22.0")
+   (version "1.24.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "GreyListChIP" version))
             (sha256
              (base32
-              "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
+              "1g9ja8p90czx83ar0l9ran7m6aggvszdbqm714fq7z4rxq9b4hs3"))))
    (properties `((upstream-name . "GreyListChIP")))
    (build-system r-build-system)
    (propagated-inputs
@@ -2765,14 +4764,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "3.0.15")
+    (version "3.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi"))))
+         "12x80z1a8gihqrlaxmzk80nc5700la72lival58s4wjv4k2lhyf3"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2840,17 +4839,49 @@ package comprehensively addressing issues ranging from post-alignments
 processing to visualization and annotation.")
     (license license:gpl2)))
 
+(define-public r-mbkmeans
+  (package
+    (name "r-mbkmeans")
+    (version "1.8.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "mbkmeans" version))
+              (sha256
+               (base32
+                "1k7ngpx4s50jplrsv19zzjr7izpdl9wwppb218ih5cp0ki1gcc2n"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-benchmarkme" ,r-benchmarkme)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-clusterr" ,r-clusterr)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/mbkmeans")
+    (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
+    (description "This package implements the mini-batch k-means algorithm for
+large datasets, including support for on-disk data representation.")
+    (license license:expat)))
+
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.46.0")
+    (version "2.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
+         "1wi15v4llgv11hpb2j9h4a35nrnawnmvbz5d5dvgy8lhqrlq8w9a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-survival" ,r-survival)
@@ -2881,13 +4912,13 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.68.0")
+    (version "1.70.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
+                "1i7s198d5kw4gk6nqqsd3vqaknj4493p822f2za8q95gv6x02rxa"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
@@ -2979,14 +5010,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.24.2")
+    (version "3.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw"))))
+         "1wnmsdrb4wz2qprj5mnd3h0wx32y2mpy3xg7mjbgwlqn9bzpw3gk"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3003,6 +5034,7 @@ determining dependencies between variables, code improvement suggestions.")
        ("r-genomicranges" ,r-genomicranges)
        ("r-ggplot2" ,r-ggplot2)
        ("r-graph" ,r-graph)
+       ("r-interactionset" ,r-interactionset)
        ("r-iranges" ,r-iranges)
        ("r-keggrest" ,r-keggrest)
        ("r-matrixstats" ,r-matrixstats)
@@ -3032,13 +5064,13 @@ enrichedGO (addGeneIDs).")
 (define-public r-matrixgenerics
   (package
    (name "r-matrixgenerics")
-   (version "1.2.1")
+   (version "1.4.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MatrixGenerics" version))
             (sha256
              (base32
-              "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
+              "1xq3a9ls125wfnhn13rdbsxzq3f6klsspx7h0znd6l67f5j5k25s"))))
    (properties
     `((upstream-name . "MatrixGenerics")))
    (build-system r-build-system)
@@ -3059,12 +5091,12 @@ incompatibilities.")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.68.0")
+    (version "1.70.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
+               (base32 "0wpmrhqpyv27h1hn31hzz21r74r7yqx79ljv8i8gn6ix8lf5ca56"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-limma" ,r-limma)))
@@ -3078,12 +5110,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.50.0")
+   (version "1.52.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
+             (base32 "1p87k4vw981k97d9bckmprrfg55jwd91658rgxzjj8hnschf28a4"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -3098,12 +5130,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.52.0")
+   (version "2.54.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
+             (base32 "1zik04y2q0anzy85l0b4ryzkxpfx2fnmpwp5s7akyk1jfl2r8gw7"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
@@ -3121,12 +5153,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
+               (base32 "1p4544xlarkbgs9kybrrawq3v7qr6ix62nrc6l7dcksh2ka69yzf"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3154,14 +5186,14 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.24.0")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
+         "0hyc0sl2nf18bz0jxbzim0v41zwh2rnnr7l3p6zkk9wnw5gn7bbc"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3180,14 +5212,14 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
+         "1kfxjh1mynrgqsy2q6byf03cbymqc8w7l7672iyd0wj5qzlif4h5"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3214,14 +5246,14 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
+         "1jmd8yrv7p7hn4gdibg3svmhqxjyrnfp7cgsqg8zv862lgd75zsl"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3255,14 +5287,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
+         "1m5w2j35wr0lzwir4s58z757vrcsj5mglsqrkvs241k0hlmn06qa"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3283,14 +5315,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "0dx6yw6rxgkcidnnyjzv57vzd112nf9n2bj6dkv7r3a2d2wj6xh4"))))
+         "034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
@@ -3317,14 +5349,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
+         "0zjl7rp5fk14kqsx0bkbpq6hqahbkiyvwa9aggp4kfb8hnmz9qal"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -3358,14 +5390,14 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
+         "1v8aysvy6a3r1iafc3xvk885c128kb3pb9zpcdhdjcn0by96k8hh"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-amap" ,r-amap)))
     (home-page "https://bioconductor.org/packages/ctc/")
@@ -3378,14 +5410,14 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
+         "07qrxssx4rb8r958r1smx8xfpzdxpp55hci3201hcmz3mxz77i0s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -3404,14 +5436,14 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
+         "0dsk8qmwimzmd1x4k4jwg9q11jm1ahn8cw0gzd6s2gmigfls4hsa"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3437,14 +5469,14 @@ information.")
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
+         "18wyi73l95df182vg3m014sxwdbpggr61vsbazhyw4vyx2fnzmpl"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3461,14 +5493,14 @@ in omics data.")
 (define-public r-plgem
   (package
     (name "r-plgem")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "plgem" version))
        (sha256
         (base32
-         "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
+         "1rz5jk5bgpk7gjknx79jyslahjg46q2f4bx6dgd0vwmarc29a45z"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -3486,14 +5518,14 @@ genes or proteins in these datasets.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
+         "0jh5db9dv5pb6b50sg22x8q55m3h0h0nkmb9mivvvp22dhyrd82z"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3533,14 +5565,14 @@ modeling the rates that determines changes in mature mRNA levels.")
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
+         "1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3562,14 +5594,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 (define-public r-ruvseq
   (package
     (name "r-ruvseq")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RUVSeq" version))
        (sha256
         (base32
-         "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
+         "1fy0k1p0m209lzjpd5jhfnifa22lrn63qq3a3kn5g0xhbbmijzac"))))
     (properties `((upstream-name . "RUVSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3590,14 +5622,14 @@ samples.")
 (define-public r-biocneighbors
   (package
     (name "r-biocneighbors")
-    (version "1.8.2")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocNeighbors" version))
        (sha256
         (base32
-         "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
+         "0cjidi18wjip9xzx83890wjk40vvjq06prf1ag4m2kac47w01r7v"))))
     (properties `((upstream-name . "BiocNeighbors")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3619,17 +5651,142 @@ to search for all neighbors within a given distance.  Parallelization is
 achieved for all methods using the BiocParallel framework.")
     (license license:gpl3)))
 
+(define-public r-scaledmatrix
+  (package
+    (name "r-scaledmatrix")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ScaledMatrix" version))
+       (sha256
+        (base32
+         "1j96fvw1waqxbv5c8myfmhsidq370z03yz13yqmrs4nn1rpn1a06"))))
+    (properties `((upstream-name . "ScaledMatrix")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-delayedarray" ,r-delayedarray)
+       ("r-matrix" ,r-matrix)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/LTLA/ScaledMatrix")
+    (synopsis "Create a DelayedMatrix of scaled and centered values")
+    (description
+     "This package provides delayed computation of a matrix of scaled and
+centered values.  The result is equivalent to using the @code{scale} function
+but avoids explicit realization of a dense matrix during block processing.
+This permits greater efficiency in common operations, most notably matrix
+multiplication.")
+    (license license:gpl3)))
+
+(define-public r-treeio
+  (package
+    (name "r-treeio")
+    (version "1.16.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "treeio" version))
+       (sha256
+        (base32
+         "0ypl4h80m08sf7r4zfvqgvpsz46x15wvcl1idq5pd813bp1w2sws"))))
+    (properties `((upstream-name . "treeio")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-dplyr" ,r-dplyr)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-magrittr" ,r-magrittr)
+       ("r-rlang" ,r-rlang)
+       ("r-tibble" ,r-tibble)
+       ("r-tidytree" ,r-tidytree)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/YuLab-SMU/treeio")
+    (synopsis "Base classes and functions for Phylogenetic tree input and output")
+    (description
+     "This is an R package to make it easier to import and store phylogenetic
+trees with associated data; and to link external data from different sources
+to phylogeny.  It also supports exporting phylogenetic trees with
+heterogeneous associated data to a single tree file and can be served as a
+platform for merging tree with associated data and converting file formats.")
+    (license license:artistic2.0)))
+
+(define-public r-ggtree
+  (package
+    (name "r-ggtree")
+    (version "3.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ggtree" version))
+       (sha256
+        (base32
+         "0i665b5jxgsv3ncxmczy7n0h911br44dw9f7m4jwv3pjmr5mm6vk"))))
+    (properties `((upstream-name . "ggtree")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-aplot" ,r-aplot)
+       ("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-magrittr" ,r-magrittr)
+       ("r-purrr" ,r-purrr)
+       ("r-rlang" ,r-rlang)
+       ("r-rvcheck" ,r-rvcheck)
+       ("r-scales" ,r-scales)
+       ("r-tidyr" ,r-tidyr)
+       ("r-tidytree" ,r-tidytree)
+       ("r-treeio" ,r-treeio)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://yulab-smu.top/treedata-book/")
+    (synopsis "R package for visualization of trees and annotation data")
+    (description
+     "This package extends the ggplot2 plotting system which implements a
+grammar of graphics.  ggtree is designed for visualization and annotation of
+phylogenetic trees and other tree-like structures with their annotation
+data.")
+    (license license:artistic2.0)))
+
+(define-public r-metapod
+  (package
+    (name "r-metapod")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "metapod" version))
+       (sha256
+        (base32
+         "1hbcwr6d8gyrf4azh0gi588xkrg6gz7gsb5hbvzqkhplbsp6shlv"))))
+    (properties `((upstream-name . "metapod")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/metapod")
+    (synopsis "Meta-analyses on p-values of differential analyses")
+    (description
+     "This package implements a variety of methods for combining p-values in
+differential analyses of genome-scale datasets.  Functions can combine
+p-values across different tests in the same analysis (e.g., genomic windows in
+ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
+analyses (e.g., replicated comparisons, effect of different treatment
+conditions).  Support is provided for handling log-transformed input p-values,
+missing values and weighting where appropriate.")
+    (license license:gpl3)))
+
 (define-public r-biocsingular
   (package
     (name "r-biocsingular")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSingular" version))
        (sha256
         (base32
-         "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
+         "1l0xgc3z5ci5sid198nsgg0k5i40rh877jybzmy0ify7rzv8carp"))))
     (properties `((upstream-name . "BiocSingular")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3641,7 +5798,8 @@ achieved for all methods using the BiocParallel framework.")
        ("r-matrix" ,r-matrix)
        ("r-rcpp" ,r-rcpp)
        ("r-rsvd" ,r-rsvd)
-       ("r-s4vectors" ,r-s4vectors)))
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scaledmatrix" ,r-scaledmatrix)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/LTLA/BiocSingular")
@@ -3700,14 +5858,14 @@ maps.")
 (define-public r-savr
   (package
     (name "r-savr")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "savR" version))
        (sha256
         (base32
-         "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
+         "1ynp334hm76zf05j4f6vha6r16s5f2ncxx9yviq4rxidk9r723jq"))))
     (properties `((upstream-name . "savR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3726,14 +5884,14 @@ Viewer (SAV) files, access data, and generate QC plots.")
 (define-public r-chipexoqual
   (package
     (name "r-chipexoqual")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPexoQual" version))
        (sha256
         (base32
-         "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
+         "0fbrf5s6pz115djm7xw95k1d0p7svi40aacbb3d52wmx5azwj424"))))
     (properties `((upstream-name . "ChIPexoQual")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3766,13 +5924,13 @@ sequencing data.")
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
+                "03pvjzjrcsbjfw3855s3whfzin45vaipy7cahnj6fywdysvh8hps"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-s4vectors" ,r-s4vectors)
@@ -3789,14 +5947,14 @@ penalized least squares regression method.")
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNAcopy" version))
        (sha256
         (base32
-         "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
+         "0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d"))))
     (properties `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
@@ -3889,14 +6047,14 @@ and regression inferences from RNA-sequencing data.")
 (define-public r-ebseq
   (package
     (name "r-ebseq")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBSeq" version))
        (sha256
         (base32
-         "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
+         "0h5v3vrb90zim80bdnr3aw58g3h7zjqa4l9i0jwx5j19ywf54fdz"))))
     (properties `((upstream-name . "EBSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3913,13 +6071,13 @@ gene and isoform level using RNA-seq data")
 (define-public r-karyoploter
   (package
     (name "r-karyoploter")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "karyoploteR" version))
               (sha256
                (base32
-                "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
+                "11sgxz2xz685pgm8mf0hzm6aryx4fj5g3dlffjzpqxh3awfqa19p"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -3951,14 +6109,14 @@ coordinates.")
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lpsymphony" version))
        (sha256
         (base32
-         "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
+         "0aw4b3p5z8ys7zlwy8s3bsqk03xwx42311yxr7q14w3f7sn3shzn"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -3981,14 +6139,14 @@ to install interface to SYMPHONY.")
 (define-public r-ihw
   (package
     (name "r-ihw")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IHW" version))
        (sha256
         (base32
-         "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
+         "0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw"))))
     (properties `((upstream-name . "IHW")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4013,14 +6171,14 @@ independent of the p-value under the null hypothesis.")
 (define-public r-icobra
   (package
     (name "r-icobra")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iCOBRA" version))
        (sha256
         (base32
-         "183asczy9v2v1vrzxb7n7pa2yfzym3l24r3737k0jg6hnp2bpw50"))))
+         "190rkx3sivj68in36hhin5v535yd6fvlvm7l90w1bl38zpb7p6jn"))))
     (properties `((upstream-name . "iCOBRA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4049,14 +6207,14 @@ interactive exploration of results.")
 (define-public r-mast
   (package
     (name "r-mast")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MAST" version))
        (sha256
         (base32
-         "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
+         "1gkpagam5rap36viyr3n4psa658x9vckrxap1h67jasiiyrcfz2d"))))
     (properties `((upstream-name . "MAST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4084,14 +6242,14 @@ single cell assay data.")
 (define-public r-monocle
   (package
     (name "r-monocle")
-    (version "2.18.0")
+    (version "2.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "monocle" version))
        (sha256
         (base32
-         "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
+         "05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -4203,14 +6361,14 @@ qPCR data, but could be used with other types as well.")
 (define-public r-noiseq
   (package
     (name "r-noiseq")
-    (version "2.34.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "NOISeq" version))
        (sha256
         (base32
-         "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
+         "18d51dv2ygsm7kkwal341f1wrwrazyns0045j00vld367kic8jiz"))))
     (properties `((upstream-name . "NOISeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4230,14 +6388,14 @@ assumptions.")
 (define-public r-scdd
   (package
     (name "r-scdd")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDD" version))
        (sha256
         (base32
-         "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
+         "1dw9m3m99apmbs32461c6lnmy81n5hxbhz3p8jk419gajkh4v1ji"))))
     (properties `((upstream-name . "scDD")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4268,14 +6426,14 @@ distributions.")
 (define-public r-scone
   (package
     (name "r-scone")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scone" version))
        (sha256
         (base32
-         "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
+         "1wlky6nkdpz8fya81l6zaxlxc30wyp2gkyh94y5995jwddll38z5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-aroma-light" ,r-aroma-light)
@@ -4290,12 +6448,14 @@ distributions.")
        ("r-gplots" ,r-gplots)
        ("r-hexbin" ,r-hexbin)
        ("r-limma" ,r-limma)
+       ("r-matrixgenerics" ,r-matrixgenerics)
        ("r-matrixstats" ,r-matrixstats)
        ("r-mixtools" ,r-mixtools)
        ("r-rarpack" ,r-rarpack)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rhdf5" ,r-rhdf5)
        ("r-ruvseq" ,r-ruvseq)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
        ("r-summarizedexperiment" ,r-summarizedexperiment)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -4310,14 +6470,14 @@ high-throughput analyses.")
 (define-public r-geoquery
   (package
     (name "r-geoquery")
-    (version "2.58.0")
+    (version "2.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GEOquery" version))
        (sha256
         (base32
-         "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
+         "0jhkdbcd03d5n8vn3xkad6f21xjkawyxc9rdwcj8vwc8alx730am"))))
     (properties `((upstream-name . "GEOquery")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4343,14 +6503,14 @@ the bridge between GEO and BioConductor.")
 (define-public r-illuminaio
   (package
     (name "r-illuminaio")
-    (version "0.32.0")
+    (version "0.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "illuminaio" version))
        (sha256
         (base32
-         "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
+         "1sy0i3nbzsw4ymdxaiwpyx1vcg9yp3i8xfjcymqwhv95j3kyglv9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-base64" ,r-base64)))
@@ -4364,14 +6524,14 @@ files, including IDAT.")
 (define-public r-siggenes
   (package
     (name "r-siggenes")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "siggenes" version))
        (sha256
         (base32
-         "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
+         "0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -4390,14 +6550,14 @@ Bayes Analyses of Microarrays} (EBAM).")
 (define-public r-bumphunter
   (package
     (name "r-bumphunter")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bumphunter" version))
        (sha256
         (base32
-         "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
+         "0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -4424,14 +6584,14 @@ studies.")
 (define-public r-minfi
   (package
     (name "r-minfi")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minfi" version))
        (sha256
         (base32
-         "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
+         "189lzppvrz6bw2kpppawgsfjyh2ahyy8bi9z8srpas67qf2r8jmj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beanplot" ,r-beanplot)
@@ -4475,14 +6635,14 @@ methylation arrays.")
 (define-public r-methylumi
   (package
     (name "r-methylumi")
-    (version "2.36.0")
+    (version "2.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "methylumi" version))
        (sha256
         (base32
-         "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
+         "1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)
@@ -4521,14 +6681,14 @@ and Infinium HD arrays are also included.")
 (define-public r-lumi
   (package
     (name "r-lumi")
-    (version "2.42.0")
+    (version "2.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lumi" version))
        (sha256
         (base32
-         "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
+         "0qjdxjdzfnnxcm07bf51v38388s5qf1i03l1sdb9jf3gxdh8yh02"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)
@@ -4560,14 +6720,14 @@ especially Illumina Infinium methylation microarrays.")
 (define-public r-linnorm
   (package
     (name "r-linnorm")
-    (version "2.14.0")
+    (version "2.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Linnorm" version))
        (sha256
         (base32
-         "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
+         "035hrniycqadmkwg8rmzw8szv0amhy31390izy91rfrld31v2yy7"))))
     (properties `((upstream-name . "Linnorm")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4621,14 +6781,14 @@ evaluation of DEG analysis methods.")
 (define-public r-ioniser
   (package
     (name "r-ioniser")
-    (version "2.14.0")
+    (version "2.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IONiseR" version))
        (sha256
         (base32
-         "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
+         "0fknlwdfd49v09zspg0337b0zzc8hqza3563yrw51viw3g35d6q3"))))
     (properties `((upstream-name . "IONiseR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4715,6 +6875,52 @@ Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
 published results; and a routine for graphical display.")
     (license license:gpl2)))
 
+(define-public r-tradeseq
+  (package
+   (name "r-tradeseq")
+   (version "1.6.0")
+   (source (origin
+            (method url-fetch)
+            (uri (bioconductor-uri "tradeSeq" version))
+            (sha256
+             (base32
+              "0fgmb309pvqf3chdhqgbd4lzhahcj5g71sica33nzn98qhipldx7"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-biobase" ,r-biobase)
+      ("r-biocparallel" ,r-biocparallel)
+      ("r-edger" ,r-edger)
+      ("r-ggplot2" ,r-ggplot2)
+      ("r-igraph" ,r-igraph)
+      ("r-magrittr" ,r-magrittr)
+      ("r-matrix" ,r-matrix)
+      ("r-matrixstats" ,r-matrixstats)
+      ("r-mgcv" ,r-mgcv)
+      ("r-monocle" ,r-monocle)
+      ("r-pbapply" ,r-pbapply)
+      ("r-princurve" ,r-princurve)
+      ("r-rcolorbrewer" ,r-rcolorbrewer)
+      ("r-s4vectors" ,r-s4vectors)
+      ("r-singlecellexperiment" ,r-singlecellexperiment)
+      ("r-slingshot" ,r-slingshot)
+      ("r-summarizedexperiment" ,r-summarizedexperiment)
+      ("r-tibble" ,r-tibble)
+      ("r-viridis" ,r-viridis)))
+   (native-inputs
+    `(("r-knitr" ,r-knitr)))
+   (home-page "https://statomics.github.io/tradeSeq/index.html")
+   (synopsis "Trajectory-based differential expression analysis")
+   (description
+    "This package provides a flexible method for fitting regression models that
+can be used to find genes that are differentially expressed along one or
+multiple lineages in a trajectory.  Based on the fitted models, it uses a
+variety of tests suited to answer different questions of interest, e.g.  the
+discovery of genes for which expression is associated with pseudotime, or which
+are differentially expressed (in a specific region) along the trajectory.  It
+fits a negative binomial generalized additive model (GAM) for each gene, and
+performs inference on the parameters of the GAM.")
+   (license license:expat)))
+
 (define-public r-triform
   (package
     (name "r-triform")
@@ -4742,14 +6948,14 @@ peak definition in combination with known profile characteristics.")
 (define-public r-varianttools
   (package
     (name "r-varianttools")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantTools" version))
        (sha256
         (base32
-         "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
+         "1gpzrln2clfrja8rzxhsis6bi1xqglh3h2lhvqlnrx4lqxhbkv9c"))))
     (properties `((upstream-name . "VariantTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4782,14 +6988,14 @@ gmapR.")
 (define-public r-heatplus
   (package
     (name "r-heatplus")
-    (version "2.36.0")
+    (version "3.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Heatplus" version))
        (sha256
         (base32
-         "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
+         "0xwg3sxmihg3p6v3nxgrqy0nrqxi6razg3b3rjh2gcb2vv8gcqng"))))
     (properties `((upstream-name . "Heatplus")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4807,14 +7013,14 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.16.1")
+    (version "2.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
+         "1fzmaxjzyvq6xj5ny1sjijdwi4krzjgyaz52fczpwrxijq5pnyn1"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4836,14 +7042,14 @@ sets of GO terms, gene products and gene clusters.")
 (define-public r-anota
   (package
     (name "r-anota")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anota" version))
        (sha256
         (base32
-         "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
+         "039bmcv5l44gszb6xapbihp3mfqdaaa8mfc05y702p78i7x93g5y"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-multtest" ,r-multtest)
@@ -4867,14 +7073,14 @@ the data set is suitable for such analysis.")
 (define-public r-sigpathway
   (package
     (name "r-sigpathway")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "sigPathway" version))
         (sha256
           (base32
-            "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
+            "1xz5nbw5dzyah8az7mpwj8m27fsvpi2jjhfg3n27dsv8rvdncqi8"))))
     (properties `((upstream-name . "sigPathway")))
     (build-system r-build-system)
     (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
@@ -4889,14 +7095,14 @@ phenotype of interest.")
 (define-public r-fgsea
   (package
     (name "r-fgsea")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fgsea" version))
        (sha256
         (base32
-         "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
+         "1mhdgy46nxgv7v54bk9bqfy0vgjzl1law7zy718swdd762xn6g9d"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
@@ -4921,14 +7127,14 @@ to multiple hypothesis correction.")
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.16.0")
+    (version "3.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
+         "1x9cg6qlvbcdb965jh01w07ibc4lj30ikq1v312rdih3sn6zsdck"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4956,20 +7162,21 @@ data.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.10.2")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
+         "0nvjwwzpmhsfkxqrn8v1a1wcrvr3xl1wn5dy89vsrdydyv31gdc6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cowplot" ,r-cowplot)
        ("r-dose" ,r-dose)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggraph" ,r-ggraph)
+       ("r-ggtree" ,r-ggtree)
        ("r-gosemsim" ,r-gosemsim)
        ("r-igraph" ,r-igraph)
        ("r-magrittr" ,r-magrittr)
@@ -4992,14 +7199,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "3.18.1")
+    (version "4.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
+         "1lmrb6ddpx1p3kdrwszhxq6nndmbiqipzrclk64mnp63y7g50q56"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
@@ -5026,17 +7233,63 @@ All the visualization methods are developed based on ggplot2 graphics.")
 profiles (GO and KEGG) of gene and gene clusters.")
     (license license:artistic2.0)))
 
+(define-public r-clusterexperiment
+  (package
+    (name "r-clusterexperiment")
+    (version "2.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "clusterExperiment" version))
+              (sha256
+               (base32
+                "1fhmayciwn1m124b4dcs3gzbghgk9f7a7qmjnvvxc958cywcwkx5"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocsingular" ,r-biocsingular)
+       ("r-cluster" ,r-cluster)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-edger" ,r-edger)
+       ("r-hdf5array" ,r-hdf5array)
+       ("r-howmany" ,r-howmany)
+       ("r-kernlab" ,r-kernlab)
+       ("r-limma" ,r-limma)
+       ("r-locfdr" ,r-locfdr)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-mbkmeans" ,r-mbkmeans)
+       ("r-nmf" ,r-nmf)
+       ("r-phylobase" ,r-phylobase)
+       ("r-pracma" ,r-pracma)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rcpp" ,r-rcpp)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-stringr" ,r-stringr)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-zinbwave" ,r-zinbwave)))
+    (home-page "https://bioconductor.org/packages/clusterExperiment/")
+    (synopsis "Compare clusterings for single-cell sequencing")
+    (description "This package provides functionality for running and comparing
+many different clusterings of single-cell sequencing data or other large mRNA
+expression data sets.")
+    (license license:artistic2.0)))
+
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
-         "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
+         "0ipzv7wdvfqhdyjiak956qq201igsdxm6dr6rh3dj6cssgsrnrpb"))))
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5050,6 +7303,7 @@ profiles (GO and KEGG) of gene and gene clusters.")
        ("r-genefilter" ,r-genefilter)
        ("r-ggvis" ,r-ggvis)
        ("r-hwriter" ,r-hwriter)
+       ("r-magrittr" ,r-magrittr)
        ("r-mass" ,r-mass)
        ("r-mlbench" ,r-mlbench)
        ("r-pls" ,r-pls)
@@ -5070,14 +7324,14 @@ data in R and Bioconductor containers.")
 (define-public r-annaffy
   (package
     (name "r-annaffy")
-    (version "1.62.0")
+    (version "1.63.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annaffy" version))
        (sha256
         (base32
-         "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
+         "071qr68dn8k3mvwgpllbk2a4g6f6yyv2087q5rmpb22lkfvi4hwv"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -5085,11 +7339,11 @@ data in R and Bioconductor containers.")
          (add-after 'unpack 'remove-reference-to-non-free-data
            (lambda _
              (substitute* "DESCRIPTION"
-               ((", KEGG.db") ""))
-             #t)))))
+               ((", KEGG.db") "")))))))
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
+       ("r-biocmanager" ,r-biocmanager)
        ("r-dbi" ,r-dbi)
        ("r-go-db" ,r-go-db)))
     (home-page "https://bioconductor.org/packages/annaffy/")
@@ -5106,14 +7360,14 @@ It allows searching of biological metadata using various criteria.")
 (define-public r-a4core
   (package
     (name "r-a4core")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Core" version))
        (sha256
         (base32
-         "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
+         "00fi753nsayv0xspavw8r9ni1sim8ng33hp3d3kj2b8ihygd1s10"))))
     (properties `((upstream-name . "a4Core")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5131,14 +7385,14 @@ arrays.")
 (define-public r-a4classif
   (package
     (name "r-a4classif")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Classif" version))
        (sha256
         (base32
-         "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
+         "1lz85bys5dp5d1ir9c9c4wy85wkk62s14niyzzxaqrxpsji2p2iw"))))
     (properties `((upstream-name . "a4Classif")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5161,14 +7415,14 @@ Affymetrix arrays.")
 (define-public r-a4preproc
   (package
     (name "r-a4preproc")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Preproc" version))
        (sha256
         (base32
-         "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
+         "1jibm2f5glzsrvl64hxc5sf59d4w6ry0f663p619hfr44mi1mpri"))))
     (properties `((upstream-name . "a4Preproc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5186,14 +7440,14 @@ is used for preprocessing the arrays.")
 (define-public r-a4reporting
   (package
     (name "r-a4reporting")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Reporting" version))
        (sha256
         (base32
-         "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
+         "09jjfby5znmg2fdkhpbinx2v21zrfa44qq7cylcn9ipffqx3pk86"))))
     (properties `((upstream-name . "a4Reporting")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5210,14 +7464,14 @@ provides reporting features.")
 (define-public r-a4base
   (package
     (name "r-a4base")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Base" version))
        (sha256
         (base32
-         "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
+         "101w4i0w8n7qhki22qr8l8wk8w6zalzmcywqm2g4238qv7xbnr8p"))))
     (properties `((upstream-name . "a4Base")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5241,14 +7495,14 @@ Affymetrix arrays.")
 (define-public r-a4
   (package
     (name "r-a4")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4" version))
        (sha256
         (base32
-         "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
+         "0bwn185admy5k99fkd2dhhvy7x1f75r0mqn5k24dbbg0paw6nnr8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-a4base" ,r-a4base)
@@ -5266,14 +7520,14 @@ Affymetrix arrays.")
 (define-public r-abseqr
   (package
     (name "r-abseqr")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "abseqR" version))
        (sha256
         (base32
-         "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
+         "1xvk84gd1lfq1icrfwwd6y79zywrisfnc3knprigzzax31aks32c"))))
     (properties `((upstream-name . "abseqR")))
     (build-system r-build-system)
     (inputs
@@ -5314,14 +7568,14 @@ further downstream analysis on its output.")
 (define-public r-bacon
   (package
     (name "r-bacon")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bacon" version))
        (sha256
         (base32
-         "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
+         "1yp0675n1g8rxdjdd7w8al5c9jq96h0kfm8218mc50z0p2fasgbj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
@@ -5341,14 +7595,14 @@ fitting a three-component normal mixture on z-scores.")
 (define-public r-rgadem
   (package
     (name "r-rgadem")
-    (version "2.38.0")
+    (version "2.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32
-         "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
+         "05drbhjqn5kik6k4h03vr3d2b6pv5rm65lsnkyx4caxxcdii4jzm"))))
     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5399,12 +7653,12 @@ distributions, modules and filter motifs.")
 (define-public r-motifdb
   (package
    (name "r-motifdb")
-   (version "1.32.0")
+   (version "1.34.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MotifDb" version))
             (sha256
-             (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
+             (base32 "04cmgg5mw1cqbg95zyfc2imykmdxyff16w26rq97xghcxwiq2b3z"))))
    (properties `((upstream-name . "MotifDb")))
    (build-system r-build-system)
    (propagated-inputs
@@ -5426,12 +7680,12 @@ frequency matrices from nine public sources, for multiple organisms.")
 (define-public r-motifbreakr
   (package
    (name "r-motifbreakr")
-   (version "2.4.0")
+   (version "2.6.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "motifbreakR" version))
             (sha256
-             (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
+             (base32 "0i18qriznad4lr6ynzmz01k5yavs5m3h7hd0adbyg8lppbzm6hh4"))))
    (properties `((upstream-name . "motifbreakR")))
    (build-system r-build-system)
    (propagated-inputs
@@ -5477,14 +7731,14 @@ Bioconductor.")
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifStack" version))
        (sha256
         (base32
-         "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
+         "0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp"))))
     (properties `((upstream-name . "motifStack")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5508,14 +7762,14 @@ type and symbol colors.")
 (define-public r-genomicscores
   (package
     (name "r-genomicscores")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicScores" version))
        (sha256
         (base32
-         "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
+         "1b8982fj0r7igj749wljsdfn3c985w8n3d5gbhr5rw73llfb8x6w"))))
     (properties `((upstream-name . "GenomicScores")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5545,14 +7799,14 @@ position-specific scores within R and Bioconductor.")
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.14.4")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
+         "168g3xkhjzrfjpa1ynifdyfhsxx3rpyrbybsarlzr9kslw1cdkxl"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5592,14 +7846,14 @@ footprints.")
 (define-public r-gofuncr
   (package
     (name "r-gofuncr")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOfuncR" version))
        (sha256
         (base32
-         "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
+         "0lp2gmjlsk1yqxim5pi26i27iijw11lrcxmji7ynlag359yfnynd"))))
     (properties `((upstream-name . "GOfuncR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5641,14 +7895,14 @@ annotations and ontologies.")
 (define-public r-abaenrichment
   (package
     (name "r-abaenrichment")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ABAEnrichment" version))
        (sha256
         (base32
-         "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
+         "15v5n6d3mnj9d86swkh9agfvrsd065dldaywm1adwmkhhk525wmd"))))
     (properties `((upstream-name . "ABAEnrichment")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5698,14 +7952,14 @@ different identifieres using the Biocore Data Team data-packages (e.g.
 (define-public r-annotationtools
   (package
     (name "r-annotationtools")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotationTools" version))
        (sha256
         (base32
-         "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
+         "18dd8saqx17fplvv5sbfz4p9fy7ksy3n9348rd3qlczihcrh9i3w"))))
     (properties
      `((upstream-name . "annotationTools")))
     (build-system r-build-system)
@@ -5723,14 +7977,14 @@ text files).")
 (define-public r-allelicimbalance
   (package
     (name "r-allelicimbalance")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AllelicImbalance" version))
        (sha256
         (base32
-         "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
+         "1mn6975npncmfjlpjs3s2pgsrm32xgvnyl2vh1922l6vra97dkrc"))))
     (properties
      `((upstream-name . "AllelicImbalance")))
     (build-system r-build-system)
@@ -5766,14 +8020,14 @@ investigation using RNA-seq data.")
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
+         "0qdac3qalcki20r90k40cc8d0lfywzn9pffg9d719yvs7nrsfdjr"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5805,14 +8059,14 @@ needed.")
 (define-public r-ebimage
   (package
     (name "r-ebimage")
-    (version "4.32.0")
+    (version "4.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBImage" version))
        (sha256
         (base32
-         "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
+         "1z3cxxg593d66nczz5hh2hdj1d87wc0lxrzc5sn6bp43n351q8h3"))))
     (properties `((upstream-name . "EBImage")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5844,14 +8098,14 @@ visualization with image data.")
 (define-public r-yamss
   (package
     (name "r-yamss")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yamss" version))
        (sha256
         (base32
-         "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
+         "1al615x778h17jqiyhiyf6djaq9iygs1hlbrna6y4xc0f2kvgxld"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -5878,14 +8132,14 @@ analysis.")
 (define-public r-gtrellis
   (package
     (name "r-gtrellis")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gtrellis" version))
        (sha256
         (base32
-         "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
+         "0l5271cpzjlm4m0v6xcdg2vxlbhn53x1fd59ynb9jwll93av5h1f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-circlize" ,r-circlize)
@@ -5907,14 +8161,14 @@ genomic categories and to add self-defined graphics in the plot.")
 (define-public r-somaticsignatures
   (package
     (name "r-somaticsignatures")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SomaticSignatures" version))
        (sha256
         (base32
-         "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
+         "0jr11c9hz7m49xc8pi6xrr5fhbv68vafvqpzhr0pmm51vvr1vfs9"))))
     (properties
      `((upstream-name . "SomaticSignatures")))
     (build-system r-build-system)
@@ -5946,14 +8200,14 @@ decomposition algorithms.")
 (define-public r-yapsa
   (package
     (name "r-yapsa")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "YAPSA" version))
        (sha256
         (base32
-         "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
+         "1xfkgjlm0rxz82qcaqzx95cwirxifd9dsswjg3zcqmz03v7a0gz2"))))
     (properties `((upstream-name . "YAPSA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5995,14 +8249,14 @@ provided.")
 (define-public r-gcrma
   (package
     (name "r-gcrma")
-    (version "2.62.0")
+    (version "2.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gcrma" version))
        (sha256
         (base32
-         "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
+         "1z4abw9s2hs3csnx25nli7fpvb3rh3l0swzl0wfqp087fcs78pxi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-affy" ,r-affy)
@@ -6081,14 +8335,14 @@ chips with the MAQC reference datasets.")
 (define-public r-quantro
   (package
     (name "r-quantro")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "quantro" version))
        (sha256
         (base32
-         "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
+         "1fkma2ic448h2lrlza8ipg65gpfsz4fhlxcnjpmzhhmzp2xi2p4a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -6114,14 +8368,14 @@ groups.")
 (define-public r-yarn
   (package
     (name "r-yarn")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yarn" version))
        (sha256
         (base32
-         "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
+         "1x07l255x52z6cgdc2j8285shqszhr034xm5686rp6d35vah55ji"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -6151,14 +8405,14 @@ large RNA-seq experiments.")
 (define-public r-roar
   (package
     (name "r-roar")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "roar" version))
        (sha256
         (base32
-         "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
+         "0vp0n90rvjm8rzwkbrxa3fasb9val56bz2srz72xwsl3jzb5yk6w"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -6219,14 +8473,14 @@ genes.")
 (define-public r-massspecwavelet
   (package
     (name "r-massspecwavelet")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MassSpecWavelet" version))
        (sha256
         (base32
-         "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
+         "1cs32sig1yvqn9xs0cvhfpmkh2lbllx7aab80sz58x03wnx8v60z"))))
     (properties
      `((upstream-name . "MassSpecWavelet")))
     (build-system r-build-system)
@@ -6243,14 +8497,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.12.0")
+    (version "3.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
+         "1fs72lkgz1jik1smi6bb4f8jh6rrlpxdh3a5hydrnnndfxkz5kwx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -6283,14 +8537,14 @@ data for high-throughput, untargeted analyte profiling.")
 (define-public r-wrench
   (package
     (name "r-wrench")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Wrench" version))
        (sha256
         (base32
-         "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
+         "0yssmqayaryrc0asjjqxdipqdfg309llrzldx38jrfgdsza6bvs0"))))
     (properties `((upstream-name . "Wrench")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6309,14 +8563,14 @@ that arising from 16s metagenomic surveys.")
 (define-public r-wiggleplotr
   (package
     (name "r-wiggleplotr")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wiggleplotr" version))
        (sha256
         (base32
-         "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
+         "13f3g6fcc29k0g21mhnypm3nc6qqjw867vamvfkdzynspsfb32ga"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -6343,14 +8597,14 @@ visualization of exonic read coverage.")
 (define-public r-widgettools
   (package
     (name "r-widgettools")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "widgetTools" version))
        (sha256
         (base32
-         "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
+         "186xgpgyfyi4angxhz6558lfpzvvszzlpyfr8xnbccs3gshk3db2"))))
     (properties `((upstream-name . "widgetTools")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/widgetTools/")
@@ -6364,14 +8618,14 @@ widgets in R.")
 (define-public r-webbioc
   (package
     (name "r-webbioc")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "webbioc" version))
        (sha256
         (base32
-         "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
+         "1mpdw477j78s2nvlf2lzm6mdjcpamyyazjn060h9q3apawn6zajx"))))
     (build-system r-build-system)
     (inputs
      `(("netpbm" ,netpbm)
@@ -6394,17 +8648,50 @@ deployed as a centralized bioinformatics resource for use by many users.
 Currently only Affymetrix oligonucleotide analysis is supported.")
     (license license:gpl2+)))
 
+(define-public r-zinbwave
+  (package
+    (name "r-zinbwave")
+    (version "1.14.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "zinbwave" version))
+       (sha256
+        (base32
+         "0xgjbk35wl1vjqyq4y5c7hna8hkgmf56xjaxcph9bs2q7mbdnqwf"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-edger" ,r-edger)
+       ("r-genefilter" ,r-genefilter)
+       ("r-matrix" ,r-matrix)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-softimpute" ,r-softimpute)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/zinbwave")
+    (synopsis "Zero-inflated negative binomial model for RNA-seq data")
+    (description "This package implements a general and flexible zero-inflated
+negative binomial model that can be used to provide a low-dimensional
+representations of single-cell RNA-seq data.  The model accounts for zero
+inflation (dropouts), over-dispersion, and the count nature of the data.
+The model also accounts for the difference in library sizes and optionally
+for batch effects and/or other covariates, avoiding the need for pre-normalize
+the data.")
+    (license license:artistic2.0)))
+
 (define-public r-zfpkm
   (package
     (name "r-zfpkm")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zFPKM" version))
        (sha256
         (base32
-         "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
+         "1k7xaxr2gn26y8bps5l32g2axfhdn07nbk4q3qcx32d5jm75qkx2"))))
     (properties `((upstream-name . "zFPKM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6426,14 +8713,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
 (define-public r-rbowtie2
   (package
     (name "r-rbowtie2")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie2" version))
        (sha256
         (base32
-         "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
+         "0r5yqjal48xlcv5cidi7p3zwygvsllmv2zzkwkc9kfq083l2i4ih"))))
     (properties `((upstream-name . "Rbowtie2")))
     (build-system r-build-system)
     (inputs
@@ -6451,14 +8738,14 @@ rapid adapter trimming, identification, and read merging.")
 (define-public r-progeny
   (package
     (name "r-progeny")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "progeny" version))
        (sha256
         (base32
-         "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
+         "10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -6481,14 +8768,14 @@ expression\".")
 (define-public r-arrmnormalization
   (package
     (name "r-arrmnormalization")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ARRmNormalization" version))
        (sha256
         (base32
-         "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
+         "0ni3vblcadhwxaq1pf1n9jn66cp3bqch68ww4c8zh19zagil2y7r"))))
     (properties
      `((upstream-name . "ARRmNormalization")))
     (build-system r-build-system)
@@ -6504,14 +8791,14 @@ Infinium HumanMethylation 450k assay.")
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "1.14.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
+         "0ymg4hmabk233qgassld62achjylm12rnidxbakfkx4dvvlbhxxv"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6519,6 +8806,7 @@ Infinium HumanMethylation 450k assay.")
        ("r-dbi" ,r-dbi)
        ("r-dbplyr" ,r-dbplyr)
        ("r-dplyr" ,r-dplyr)
+       ("r-filelock" ,r-filelock)
        ("r-httr" ,r-httr)
        ("r-rappdirs" ,r-rappdirs)
        ("r-rsqlite" ,r-rsqlite)))
@@ -6536,14 +8824,14 @@ and data files used across sessions.")
 (define-public r-iclusterplus
   (package
     (name "r-iclusterplus")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iClusterPlus" version))
        (sha256
         (base32
-         "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
+         "1haj25c4cmmjjvh181b41a9pvkh92f7k2w4ljn17iqg31vm45za1"))))
     (properties `((upstream-name . "iClusterPlus")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
@@ -6566,14 +8854,14 @@ Gaussian distributions.")
 (define-public r-rbowtie
   (package
     (name "r-rbowtie")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie" version))
        (sha256
         (base32
-         "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
+         "0mfikbrs28q7r3lnsq0jma5x6nkrnm3q46242jh35w9c969jk5yy"))))
     (properties `((upstream-name . "Rbowtie")))
     (build-system r-build-system)
     (inputs
@@ -6591,14 +8879,14 @@ alignment tool.")
 (define-public r-sgseq
   (package
     (name "r-sgseq")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SGSeq" version))
        (sha256
         (base32
-         "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
+         "0i1yaw8h8gibakvaf1xd6nnjx2bsb2s9c0q74rbq9lm7haihivp6"))))
     (properties `((upstream-name . "SGSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6634,14 +8922,14 @@ interpretation.")
 (define-public r-rhisat2
   (package
     (name "r-rhisat2")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhisat2" version))
        (sha256
         (base32
-         "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
+         "1hqahh5h22mj2crqp6r9xnm111xmfgk39c100rcaziqrpdy5npk8"))))
     (properties `((upstream-name . "Rhisat2")))
     (build-system r-build-system)
     (arguments
@@ -6674,14 +8962,14 @@ index.")
 (define-public r-quasr
   (package
     (name "r-quasr")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "QuasR" version))
        (sha256
         (base32
-         "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
+         "1635ff11ahzjrh3cdcxrq5bgd100n444k7mc0maz0jx21vj8qqb1"))))
     (properties `((upstream-name . "QuasR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6693,13 +8981,11 @@ index.")
        ("r-biostrings" ,r-biostrings)
        ("r-bsgenome" ,r-bsgenome)
        ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomicfiles" ,r-genomicfiles)
        ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
        ("r-rbowtie" ,r-rbowtie)
-       ("r-rhisat2" ,r-rhisat2)
        ("r-rhtslib" ,r-rhtslib)
        ("r-rsamtools" ,r-rsamtools)
        ("r-rtracklayer" ,r-rtracklayer)
@@ -6719,14 +9005,14 @@ quantification of genomic regions of interest.")
 (define-public r-rqc
   (package
     (name "r-rqc")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rqc" version))
        (sha256
         (base32
-         "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
+         "02hwj2vd003x0zf273ndnwh7kxy6wc3sz14d3kryp2w2aqjj826f"))))
     (properties `((upstream-name . "Rqc")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6762,14 +9048,14 @@ graphics.")
 (define-public r-birewire
   (package
     (name "r-birewire")
-    (version "3.22.0")
+    (version "3.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiRewire" version))
        (sha256
         (base32
-         "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
+         "0p6mr67mkw54490sv4dvkyh8l0xkpjfbqy532vi8l41i40qg3gry"))))
     (properties `((upstream-name . "BiRewire")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6820,14 +9106,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.")
 (define-public r-multidataset
   (package
     (name "r-multidataset")
-    (version "1.18.2")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiDataSet" version))
        (sha256
         (base32
-         "1wzhxgprriicw6lx1h91z4r9d5yaxar859scp83bm8pr9aznqk2z"))))
+         "1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj"))))
     (properties `((upstream-name . "MultiDataSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6857,14 +9143,14 @@ packages.")
 (define-public r-ropls
   (package
     (name "r-ropls")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32
-         "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
+         "1j99kdywyljqzdcns5ysh590w4w8iiwzpddpfk5c8d4whax7vk5b"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -6895,14 +9181,14 @@ coefficients).")
 (define-public r-biosigner
   (package
     (name "r-biosigner")
-    (version "1.18.2")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biosigner" version))
        (sha256
         (base32
-         "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
+         "159fbkymn92li7dinsm56nsacjp8wnhsljv7airgs9m82p8wd5sl"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
@@ -6928,14 +9214,14 @@ datasets.")
 (define-public r-annotatr
   (package
     (name "r-annotatr")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotatr" version))
        (sha256
         (base32
-         "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
+         "0pcf4jrq05bmfxph41hmdx1x147k1ay5fl2h488y1s4h8qm3c67p"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -6969,14 +9255,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.4.3")
+    (version "2.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba"))))
+         "007pbvxkhh930zdkgjaihannjbpbfnbizp3ffc2vyxygw0r4vz68"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -6995,14 +9281,14 @@ and to both short and long sequence reads.")
 (define-public r-flowutils
   (package
     (name "r-flowutils")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowUtils" version))
        (sha256
         (base32
-         "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
+         "1sdwgyvrsz0pp60zdfrcgb7bs8s87j7257p8ck813ydizc324x9w"))))
     (properties `((upstream-name . "flowUtils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7021,14 +9307,14 @@ and to both short and long sequence reads.")
 (define-public r-consensusclusterplus
   (package
     (name "r-consensusclusterplus")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ConsensusClusterPlus" version))
        (sha256
         (base32
-         "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
+         "163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b"))))
     (properties
      `((upstream-name . "ConsensusClusterPlus")))
     (build-system r-build-system)
@@ -7046,30 +9332,18 @@ cluster count and membership by stability evidence in unsupervised analysis.")
 (define-public r-cytolib
   (package
     (name "r-cytolib")
-    (version "2.2.1")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cytolib" version))
        (sha256
         (base32
-         "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
+         "0wl7zqwv0i38dfzqfsz40n3mcbxi38ffn1rbd5pm9s7hq16zr4nv"))))
     (properties `((upstream-name . "cytolib")))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-linking
-           (lambda _
-             (substitute* "src/Makevars.in"
-               ;; This is to avoid having a plain directory on the list of
-               ;; libraries to link.
-               (("\\(RHDF5_LIBS\\)" match)
-                (string-append match "/libhdf5.a")))
-             #t)))))
     (native-inputs
-     `(("r-knitr" ,r-knitr)
-       ("pkg-config" ,pkg-config)))
+     `(("r-knitr" ,r-knitr)))
     (propagated-inputs
      `(("r-bh" ,r-bh)
        ("r-rcpp" ,r-rcpp)
@@ -7087,14 +9361,14 @@ interact with gated cytometry data.")
 (define-public r-flowcore
   (package
     (name "r-flowcore")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowCore" version))
        (sha256
         (base32
-         "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
+         "13xpbkxi53rxmhvpdiy6bydmhicmxd2gi96d9c1qx4lkss2f14nc"))))
     (properties `((upstream-name . "flowCore")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7119,14 +9393,14 @@ with flow cytometry data.")
 (define-public r-flowmeans
   (package
     (name "r-flowmeans")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowMeans" version))
        (sha256
         (base32
-         "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
+         "1awskkq48qhv4v9glxgfqi0kgwqd62fbj641k4vvxfcwsf2c7bfg"))))
     (properties `((upstream-name . "flowMeans")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7145,27 +9419,16 @@ change point detection.")
 (define-public r-ncdfflow
   (package
     (name "r-ncdfflow")
-    (version "2.36.0")
+    (version "2.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ncdfFlow" version))
        (sha256
         (base32
-         "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
+         "1lm88qnfv6rnnr7wmgbvwyj272imjjjn7h3agxqqzsbmn8vyrnf0"))))
     (properties `((upstream-name . "ncdfFlow")))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-linking
-           (lambda _
-             (substitute* "src/Makevars"
-               ;; This is to avoid having a plain directory on the list of
-               ;; libraries to link.
-               (("\\(RHDF5_LIBS\\)" match)
-                (string-append match "/libhdf5.a")))
-             #t)))))
     (propagated-inputs
      `(("r-bh" ,r-bh)
        ("r-biobase" ,r-biobase)
@@ -7187,14 +9450,14 @@ manipulation of flow cytometry data.")
 (define-public r-ggcyto
   (package
     (name "r-ggcyto")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggcyto" version))
        (sha256
         (base32
-         "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
+         "0jd6m84m4znnpix4bcgdby7mnflsn206f5x2vw9n8rxnwzx77wpg"))))
     (properties `((upstream-name . "ggcyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7224,14 +9487,14 @@ statistics to the plot.")
 (define-public r-flowviz
   (package
     (name "r-flowviz")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowViz" version))
        (sha256
         (base32
-         "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
+         "17x04xwyw2pp5zkhgvrmxkb8cbrv9wql6xhjsfpq0n6yd9dxqc1v"))))
     (properties `((upstream-name . "flowViz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7255,14 +9518,14 @@ statistics to the plot.")
 (define-public r-flowclust
   (package
     (name "r-flowclust")
-    (version "3.28.0")
+    (version "3.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowClust" version))
        (sha256
         (base32
-         "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
+         "03xsmprrkxwkaksjlaxwp54mqfb3zlg6dbqhp87w78fwscisv76b"))))
     (properties `((upstream-name . "flowClust")))
     (build-system r-build-system)
     (arguments
@@ -7295,14 +9558,14 @@ model with Box-Cox transformation.")
 (define-public r-rprotobuflib
   (package
     (name "r-rprotobuflib")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RProtoBufLib" version))
        (sha256
         (base32
-         "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
+         "1hyds97ay4mn7nl830yh9v8mlasgsljsx5wsrhz2zsmbbyx6wbnb"))))
     (properties `((upstream-name . "RProtoBufLib")))
     (build-system r-build-system)
     (arguments
@@ -7311,8 +9574,7 @@ model with Box-Cox transformation.")
          (add-after 'unpack 'unpack-bundled-sources
            (lambda _
              (with-directory-excursion "src"
-               (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
-             #t)))))
+               (invoke "tar" "xf" "protobuf-3.13.0.tar.gz")))))))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/RProtoBufLib/")
@@ -7325,27 +9587,16 @@ for other R packages to compile and link against.")
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")
-    (version "4.2.0")
+    (version "4.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32
-         "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
+         "1a9qb2dcvwgb3z0vdbbzn1rzy77d3da72kirs272344hdx9b2cx9"))))
     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-linking
-           (lambda _
-             (substitute* "src/Makevars"
-               ;; This is to avoid having a plain directory on the list of
-               ;; libraries to link.
-               (("\\{h5lib\\}" match)
-                (string-append match "/libhdf5.a")))
-             #t)))))
     (propagated-inputs
      `(("r-aws-s3" ,r-aws-s3)
        ("r-aws-signature" ,r-aws-signature)
@@ -7354,6 +9605,7 @@ for other R packages to compile and link against.")
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-cytolib" ,r-cytolib)
        ("r-data-table" ,r-data-table)
+       ("r-delayedarray" ,r-delayedarray)
        ("r-digest" ,r-digest)
        ("r-dplyr" ,r-dplyr)
        ("r-flowcore" ,r-flowcore)
@@ -7370,6 +9622,7 @@ for other R packages to compile and link against.")
        ("r-rgraphviz" ,r-rgraphviz)
        ("r-rhdf5lib" ,r-rhdf5lib)
        ("r-rprotobuflib" ,r-rprotobuflib)
+       ("r-s4vectors" ,r-s4vectors)
        ("r-scales" ,r-scales)
        ("r-xml" ,r-xml)))
     (native-inputs
@@ -7388,14 +9641,14 @@ matches the flowJo analysis.")
 (define-public r-flowstats
   (package
     (name "r-flowstats")
-    (version "4.2.0")
+    (version "4.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowStats" version))
        (sha256
         (base32
-         "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
+         "1yr5m7qmhmm52c70z3d0zy4zgf0hja7r2ig9yljv5w86bzm962x6"))))
     (properties `((upstream-name . "flowStats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7424,14 +9677,14 @@ package.")
 (define-public r-opencyto
   (package
     (name "r-opencyto")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "openCyto" version))
        (sha256
         (base32
-         "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
+         "1par1d5pk1rjg15q7i5z5wqma7xg6fycb826a823wk8wr52a885x"))))
     (properties `((upstream-name . "openCyto")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7468,27 +9721,16 @@ sequential way to mimic the manual gating strategy.")
 (define-public r-cytoml
   (package
     (name "r-cytoml")
-    (version "2.2.2")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CytoML" version))
        (sha256
         (base32
-         "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1"))))
+         "0ixy7mmnipk8wy61wz6qy7jfbc5zhs6p5iqaii8hdprjnb841ri7"))))
     (properties `((upstream-name . "CytoML")))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-linking
-           (lambda _
-             (substitute* "src/Makevars.in"
-               ;; This is to avoid having a plain directory on the list of
-               ;; libraries to link.
-               (("\\{h5lib\\}" match)
-                (string-append match "/libhdf5.a")))
-             #t)))))
     (inputs
      `(("libxml2" ,libxml2)
        ("zlib" ,zlib)))
@@ -7532,25 +9774,38 @@ standard to exchange gated cytometry data with other software platforms.")
 (define-public r-flowsom
   (package
     (name "r-flowsom")
-    (version "1.22.0")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "FlowSOM" version))
        (sha256
         (base32
-         "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
+         "18h7p7g3w9imyd1c93jllgp4kd74z96cs85wcqfhmd26nx18hl82"))))
     (properties `((upstream-name . "FlowSOM")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-colorramps" ,r-colorramps)
        ("r-consensusclusterplus" ,r-consensusclusterplus)
        ("r-cytoml" ,r-cytoml)
+       ("r-dplyr" ,r-dplyr)
        ("r-flowcore" ,r-flowcore)
        ("r-flowworkspace" ,r-flowworkspace)
+       ("r-ggforce" ,r-ggforce)
+       ("r-ggnewscale" ,r-ggnewscale)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggpointdensity" ,r-ggpointdensity)
+       ("r-ggpubr" ,r-ggpubr)
+       ("r-ggrepel" ,r-ggrepel)
        ("r-igraph" ,r-igraph)
+       ("r-magrittr" ,r-magrittr)
+       ("r-pheatmap" ,r-pheatmap)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-tsne" ,r-tsne)
+       ("r-rlang" ,r-rlang)
+       ("r-rtsne" ,r-rtsne)
+       ("r-scattermore" ,r-scattermore)
+       ("r-tidyr" ,r-tidyr)
        ("r-xml" ,r-xml)))
     (home-page "https://bioconductor.org/packages/FlowSOM/")
     (synopsis "Visualize and interpret cytometry data")
@@ -7562,14 +9817,14 @@ self-organizing map clustering and minimal spanning trees.")
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.14.1")
+    (version "6.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "07d1z33bc3bym1jwp1qqfhs18w4v9axk0ycnmldmj6piswvp44wk"))))
+         "1hri5rrqf8vq3c6pivfamv60yz9mf9rrdpdd5bw2h24lghm2x8rw"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7608,14 +9863,14 @@ delete entire rows with missing data.")
 (define-public r-depecher
   (package                              ;Source/Weave error
     (name "r-depecher")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DepecheR" version))
        (sha256
         (base32
-         "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
+         "04vxc43p3kpsx0vksk2nwmy9p56h35z2mc8j9p2wm29zaz1y8j3p"))))
     (properties `((upstream-name . "DepecheR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7654,24 +9909,29 @@ data, to only emphasize the data that actually matters.")
 (define-public r-rcistarget
   (package
     (name "r-rcistarget")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RcisTarget" version))
        (sha256
         (base32
-         "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
+         "1yh0l11vnslgr6zsbpgc8mc4aa32zy34f5yrz98hkcdl53iw5y7f"))))
     (properties `((upstream-name . "RcisTarget")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-aucell" ,r-aucell)
+     `(("r-arrow" ,r-arrow)
+       ("r-aucell" ,r-aucell)
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-data-table" ,r-data-table)
+       ("r-dplyr" ,r-dplyr)
        ("r-feather" ,r-feather)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
        ("r-gseabase" ,r-gseabase)
        ("r-r-utils" ,r-r-utils)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-tibble" ,r-tibble)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://aertslab.org/#scenic")
@@ -7691,14 +9951,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
+         "0kw16zf9004d1zlwsswhbcb7p77nabpd1fjagznff3zyan9fpdxf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -7758,14 +10018,14 @@ accessibility data.")
 (define-public r-circrnaprofiler
   (package
     (name "r-circrnaprofiler")
-    (version "1.4.2")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "circRNAprofiler" version))
        (sha256
         (base32
-         "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
+         "1hif40vfg2lkbyf6abbkxbdm3b1biw6gxnh6ca2sydvi3y5l2ys2"))))
     (properties
      `((upstream-name . "circRNAprofiler")))
     (build-system r-build-system)
@@ -7855,17 +10115,19 @@ cisTopics and explore the nature and regulatory proteins driving them.")
 (define-public r-genie3
   (package
     (name "r-genie3")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GENIE3" version))
        (sha256
         (base32
-         "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
+         "1v54dzcz654wfm3npbp8gb55v49im0fm547cz3hvsidq4zhi3l1b"))))
     (properties `((upstream-name . "GENIE3")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-reshape2" ,r-reshape2)))
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-reshape2" ,r-reshape2)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/GENIE3")
@@ -7878,14 +10140,14 @@ regulatory networks from expression data.")
 (define-public r-roc
   (package
     (name "r-roc")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROC" version))
        (sha256
         (base32
-         "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
+         "0ff5rcpyybgjzsfbhaslim0m02n3bksv1r9v7bq0gg0iyzll0rjc"))))
     (properties `((upstream-name . "ROC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7926,14 +10188,14 @@ data.")
 (define-public r-watermelon
   (package
     (name "r-watermelon")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wateRmelon" version))
        (sha256
         (base32
-         "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
+         "1qar8z0nf33bqr488swig0bfq8lnvcdjcxvw3q3b0hkkvybn27zw"))))
     (properties `((upstream-name . "wateRmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7963,14 +10225,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
 (define-public r-gdsfmt
   (package
     (name "r-gdsfmt")
-    (version "1.26.1")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gdsfmt" version))
        (sha256
         (base32
-         "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
+         "119qdivd7vaaqkjb0nrwidi6g26hh8znhif3g4prqn7x5pl2clvy"))
        (modules '((guix build utils)))
        ;; Remove bundled sources of zlib, lz4, and xz.  Don't attempt to build
        ;; them and link with system libraries instead.
@@ -8022,14 +10284,14 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-bigmelon
   (package
     (name "r-bigmelon")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigmelon" version))
        (sha256
         (base32
-         "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
+         "061f0hc4m4nvdr6298pg3inpx1z2bpsm9nlxqs3v7n58q15xyzri"))))
     (properties `((upstream-name . "bigmelon")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8050,14 +10312,14 @@ with multiple R processes supported by the package @code{parallel}.")
 (define-public r-seqbias
   (package
     (name "r-seqbias")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqbias" version))
        (sha256
         (base32
-         "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
+         "06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k"))))
     (properties `((upstream-name . "seqbias")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8114,14 +10376,14 @@ injected in that sequence).")
 (define-public r-reqon
   (package
     (name "r-reqon")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReQON" version))
        (sha256
         (base32
-         "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
+         "1z13avbxwvvhh03arjfnaipznynifsi8k2hzw4kappz24f7lwmza"))))
     (properties `((upstream-name . "ReQON")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8139,14 +10401,14 @@ format.")
 (define-public r-wavcluster
   (package
     (name "r-wavcluster")
-    (version "2.24.0")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wavClusteR" version))
        (sha256
         (base32
-         "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
+         "1sydzrqydfv1ik2h08xkxlx6xrv866bf0if6v5wch9l3krh0sych"))))
     (properties `((upstream-name . "wavClusteR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8186,14 +10448,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
 (define-public r-timeseriesexperiment
   (package
     (name "r-timeseriesexperiment")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TimeSeriesExperiment" version))
        (sha256
         (base32
-         "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
+         "10xgihjssnc6i03819p9gnzwfc7znanic514ar3yxzl3fhxy3yyy"))))
     (properties
      `((upstream-name . "TimeSeriesExperiment")))
     (build-system r-build-system)
@@ -8227,14 +10489,14 @@ provides methods for retrieving enriched pathways.")
 (define-public r-variantfiltering
   (package
     (name "r-variantfiltering")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantFiltering" version))
        (sha256
         (base32
-         "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
+         "0abhrk53csd9jz9sv4q1qr74jax9mbj2icbz1iilf1123nvnjypd"))))
     (properties
      `((upstream-name . "VariantFiltering")))
     (build-system r-build-system)
@@ -8333,14 +10595,14 @@ arrays based on fast wavelet-based functional models.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
+         "1pqy2g9pg8pswmkrs2fzlkwwliw2r7f33h05bci5bz41b8ribpzj"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
@@ -8377,14 +10639,14 @@ measures.")
 (define-public r-htqpcr
   (package
     (name "r-htqpcr")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HTqPCR" version))
        (sha256
         (base32
-         "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
+         "1y3ik5a9w66jby6682jfm8mn2883s8yfv4xw8a8v1f6q2d1j938l"))))
     (properties `((upstream-name . "HTqPCR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8411,14 +10673,14 @@ features (e.g.  genes, microRNAs).")
 (define-public r-unifiedwmwqpcr
   (package
     (name "r-unifiedwmwqpcr")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "unifiedWMWqPCR" version))
        (sha256
         (base32
-         "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
+         "1clcz610sl3s0mjf84j21xgrmjhkxcc4h292ljwq5yzbkk68g896"))))
     (properties
      `((upstream-name . "unifiedWMWqPCR")))
     (build-system r-build-system)
@@ -8436,14 +10698,14 @@ data.")
 (define-public r-universalmotif
   (package
     (name "r-universalmotif")
-    (version "1.8.5")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "universalmotif" version))
        (sha256
         (base32
-         "07862bs771xldmdnq0zr8926dr299ach8nrgci14p5bbrc88l3ly"))))
+         "1hwp7802r4pr7yafzir9afqaim9l0vznglm35b0gxaca8k7a3jvy"))))
     (properties
      `((upstream-name . "universalmotif")))
     (build-system r-build-system)
@@ -8458,12 +10720,10 @@ data.")
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biostrings" ,r-biostrings)
        ("r-ggplot2" ,r-ggplot2)
-       ("r-ggseqlogo" ,r-ggseqlogo)
        ("r-iranges" ,r-iranges)
        ("r-mass" ,r-mass)
        ("r-rcpp" ,r-rcpp)
        ("r-rcppthread" ,r-rcppthread)
-       ("r-rdpack" ,r-rdpack)
        ("r-rlang" ,r-rlang)
        ("r-s4vectors" ,r-s4vectors)
        ("r-yaml" ,r-yaml)))
@@ -8552,14 +10812,14 @@ cellular organization in health and disease.")
 (define-public r-bgmix
   (package
     (name "r-bgmix")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BGmix" version))
        (sha256
         (base32
-         "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
+         "1gp40ddspblpszzm4k4r7ysgx883iwdfqc5ds23p2q1ml9idwgvv"))))
     (properties `((upstream-name . "BGmix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8574,14 +10834,14 @@ gene expression.")
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
+         "18n6j2ihv85rhai5sf5k3mwf9nkc2nl2sinx3rrs6sbl529g4mw4"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8599,14 +10859,14 @@ Affymetrix GeneChips.")
 (define-public r-bhc
   (package
     (name "r-bhc")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BHC" version))
        (sha256
         (base32
-         "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
+         "0aaawm7h3ppyyhd7hi14rpynagnxx4730f5vxizj5bpzwbclp6h9"))))
     (properties `((upstream-name . "BHC")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BHC/")
@@ -8625,14 +10885,14 @@ algorithm which is more efficient for larger data sets.")
 (define-public r-bicare
   (package
     (name "r-bicare")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BicARE" version))
        (sha256
         (base32
-         "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
+         "0j3gs4xcdgaca2c62jf2h86skbbxm1c9g2khs5bsa8fmkskr6vl9"))))
     (properties `((upstream-name . "BicARE")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8649,14 +10909,14 @@ results.")
 (define-public r-bifet
   (package
     (name "r-bifet")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiFET" version))
        (sha256
         (base32
-         "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
+         "1fwy7ws0bn67557s0kcw8pbln2jg834n6kfbs8297ps07nxr0lpj"))))
     (properties `((upstream-name . "BiFET")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8679,19 +10939,18 @@ the read count and GC content bias.")
 (define-public r-rsbml
   (package
     (name "r-rsbml")
-    (version "2.48.0")
+    (version "2.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rsbml" version))
        (sha256
         (base32
-         "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
+         "017xwra6ms7kx6sg3ksw1vr9zn23imc2qjgpmjikx7mgbak125xh"))))
     (properties `((upstream-name . "rsbml")))
     (build-system r-build-system)
     (inputs
-     `(("libsbml" ,libsbml)
-       ("zlib" ,zlib)))
+     `(("libsbml" ,libsbml)))
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-graph" ,r-graph)))
@@ -8707,14 +10966,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
 (define-public r-hypergraph
   (package
     (name "r-hypergraph")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hypergraph" version))
        (sha256
         (base32
-         "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
+         "01knpd964m2g9vwd7c72qnc8g2p2pzhvk7lin4mhvcmb3pvsdlh7"))))
     (properties `((upstream-name . "hypergraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8729,14 +10988,14 @@ manipulating hypergraphs.")
 (define-public r-hyperdraw
   (package
     (name "r-hyperdraw")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hyperdraw" version))
        (sha256
         (base32
-         "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
+         "1qkxixkgvvfha0ii8rwwcbrbjmbbxsy8afv5ymcq01k3hbykx44r"))))
     (properties `((upstream-name . "hyperdraw")))
     (build-system r-build-system)
     (inputs `(("graphviz" ,graphviz)))
@@ -8753,14 +11012,14 @@ manipulating hypergraphs.")
 (define-public r-biggr
   (package
     (name "r-biggr")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiGGR" version))
        (sha256
         (base32
-         "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
+         "1y9659pxm65w51zvrz36girb3qvfc64zijjkxmg6xn4pbc8vv1wf"))))
     (properties `((upstream-name . "BiGGR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8817,14 +11076,14 @@ a file-backed matrix with factor properties.")
 (define-public r-bigpint
   (package
     (name "r-bigpint")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigPint" version))
        (sha256
         (base32
-         "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
+         "0yrg9x1a92zmz7j5hk77cph1jg82mkpr7k7qi9fdr6z5nqq6fgz6"))))
     (properties `((upstream-name . "bigPint")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8860,14 +11119,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
 (define-public r-chemminer
   (package
     (name "r-chemminer")
-    (version "3.42.2")
+    (version "3.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChemmineR" version))
        (sha256
         (base32
-         "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
+         "1z59npqk7hnqzhjdnry6lfqlyxfzwqprp7bmbdzs4rp22pzcv1v8"))))
     (properties `((upstream-name . "ChemmineR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8901,14 +11160,14 @@ structures.")
 (define-public r-bioassayr
   (package
     (name "r-bioassayr")
-    (version "1.28.3")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioassayR" version))
        (sha256
         (base32
-         "03pdb76j7c28b1h1flb40ahq7i9iha22kblq6mkl3x4xmrdgaw5y"))))
+         "1mlv80w8a7l8cii3dfqvanvh0qdqvcg8c1iiq4xlyvkjxfs64ka1"))))
     (properties `((upstream-name . "bioassayR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8936,14 +11195,14 @@ available bioactivity data.")
 (define-public r-biobroom
   (package
     (name "r-biobroom")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobroom" version))
        (sha256
         (base32
-         "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
+         "1ybyhmrcvj6k1laxw9bc8jbn533frkzh9k8kl1ibd5pi368rfqzn"))))
     (properties `((upstream-name . "biobroom")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8968,14 +11227,14 @@ visualize bioinformatics analyses.")
 (define-public r-graphite
   (package
     (name "r-graphite")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "graphite" version))
        (sha256
         (base32
-         "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
+         "11bgz6951nfygxp3fm0190gf2bb5zplis1bc0am4757liw4qybhf"))))
     (properties `((upstream-name . "graphite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8984,6 +11243,8 @@ visualize bioinformatics analyses.")
        ("r-graph" ,r-graph)
        ("r-httr" ,r-httr)
        ("r-rappdirs" ,r-rappdirs)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/graphite/")
     (synopsis "Networks from pathway databases")
     (description
@@ -8995,14 +11256,14 @@ symbols).")
 (define-public r-reactomepa
   (package
     (name "r-reactomepa")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReactomePA" version))
        (sha256
         (base32
-         "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
+         "1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf"))))
     (properties `((upstream-name . "ReactomePA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9027,14 +11288,14 @@ enrichment analysis and several functions for visualization.")
 (define-public r-ebarrays
   (package
     (name "r-ebarrays")
-    (version "2.54.0")
+    (version "2.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBarrays" version))
        (sha256
         (base32
-         "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
+         "1k1kl0m7wzaqpv7i20pfav2a6jf93bhri4w7qdikmvkf011n9422"))))
     (properties `((upstream-name . "EBarrays")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9073,35 +11334,16 @@ monograph.")
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
+                "1h0l5w33c9jpc20pynq634qmx8jbfa802d7jslmf4haljmrxm4a1"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         ;; This package can be used by calling BiocCheck(<package>) from
-         ;; within R, or by running R CMD BiocCheck <package>.  This phase
-         ;; makes sure the latter works.  For this to work, the BiocCheck
-         ;; script must be somewhere on the PATH (not the R bin directory).
-         (add-after 'install 'install-bioccheck-subcommand
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (dest-dir (string-append out "/bin"))
-                    (script-dir
-                     (string-append out "/site-library/BiocCheck/script/")))
-               (mkdir-p dest-dir)
-               (symlink (string-append script-dir "/checkBadDeps.R")
-                        (string-append dest-dir "/checkBadDeps.R"))
-               (symlink (string-append script-dir "/BiocCheck")
-                        (string-append dest-dir "/BiocCheck")))
-             #t)))))
     (propagated-inputs
      `(("r-codetools" ,r-codetools)
        ("r-graph" ,r-graph)
@@ -9122,14 +11364,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
 (define-public r-biocgraph
   (package
     (name "r-biocgraph")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocGraph" version))
        (sha256
         (base32
-         "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
+         "12bmj9kdlylp02cfwviak7y323ndccl2694rvi4cdg4vsx7v3ya3"))))
     (properties `((upstream-name . "biocGraph")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9147,13 +11389,13 @@ different graph related packages produced by Bioconductor.")
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-    (version "2.18.1")
+    (version "2.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
+                "062zhy33a2c70ibqghnjxcys0wbqc998aza8nnygk4zmpd4iyy1z"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
@@ -9175,13 +11417,13 @@ functionality.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.58.1")
+    (version "1.60.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
+                "0pc5ll59vm8a9s1nrdc7p9wk11a52rrz669fsrrqd8qapa8p6wfd"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -9203,14 +11445,14 @@ also known as views, in a controlled vocabulary.")
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
-    (version "1.16.1")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ExperimentHub" version))
        (sha256
         (base32
-         "1iyf052hh2dhlwzwwrj571cwr3hd9wp2j915sqg77x6jn40wjr1g"))))
+         "1mzmw3100lf33yhz27nbxncrjk5bprlackrjcwf8xdhcaidg40p4"))))
     (properties `((upstream-name . "ExperimentHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9237,14 +11479,14 @@ access.")
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
+         "1h63vg1iskw79ijg5h1b9097ams8pp3kvnlawlfci6xfli07xpkj"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9264,14 +11506,14 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
+         "0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
@@ -9299,14 +11541,14 @@ rownames.")
 (define-public r-bioconcotk
   (package
     (name "r-bioconcotk")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocOncoTK" version))
        (sha256
         (base32
-         "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
+         "0y396lx2mh9izb07lz83j35wydfj808ihc74jlgras03a3g335p2"))))
     (properties `((upstream-name . "BiocOncoTK")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9344,14 +11586,14 @@ tools for genome-scale analysis of cancer studies.")
 (define-public r-biocor
   (package
     (name "r-biocor")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioCor" version))
        (sha256
         (base32
-         "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
+         "135rga7mwpzy8ypvriqpbmlh9l5yf61s9s1sa9615qfab14jh06b"))))
     (properties `((upstream-name . "BioCor")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9373,14 +11615,14 @@ gene selection, testing relationships, and so on.")
 (define-public r-biocpkgtools
   (package
     (name "r-biocpkgtools")
-    (version "1.8.2")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocPkgTools" version))
        (sha256
         (base32
-         "18m816mh1ic0znp38wax8xppai77lkym3w84x4x30x2mf0vriqfw"))))
+         "18a9mbzfmkipnv1cc9h3rhn9jxdp7nzywp0bz7hvmsaffv4p4skc"))))
     (properties `((upstream-name . "BiocPkgTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9397,7 +11639,6 @@ gene selection, testing relationships, and so on.")
        ("r-igraph" ,r-igraph)
        ("r-jsonlite" ,r-jsonlite)
        ("r-magrittr" ,r-magrittr)
-       ("r-rappdirs" ,r-rappdirs)
        ("r-rbgl" ,r-rbgl)
        ("r-readr" ,r-readr)
        ("r-rex" ,r-rex)
@@ -9423,14 +11664,14 @@ analytics on packages.")
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
+         "18zr0r4b4rblfmsiilipqdfxn9fgymx75hlxzx1wk3bm71ryk078"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9461,14 +11702,14 @@ accessing web references for elements/sets are also available in BiocSet.")
 (define-public r-biocworkflowtools
   (package
     (name "r-biocworkflowtools")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocWorkflowTools" version))
        (sha256
         (base32
-         "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
+         "1a32bwgnxaw0gv2gij2p4rm0a6l06jjhidvfz2v4k900pz1w79av"))))
     (properties
      `((upstream-name . "BiocWorkflowTools")))
     (build-system r-build-system)
@@ -9494,14 +11735,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
 (define-public r-biodist
   (package
     (name "r-biodist")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioDist" version))
        (sha256
         (base32
-         "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
+         "1y1x9q9aa76gbhsyfn638rxp5icjvq30fv3a4205xh7g5jwlf6yw"))))
     (properties `((upstream-name . "bioDist")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9517,14 +11758,14 @@ distance measures.")
 (define-public r-pcatools
   (package
     (name "r-pcatools")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "PCAtools" version))
        (sha256
         (base32
-         "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
+         "11idi9fwvyhkakbm63qxcdhkany8gbskis04z0p5a39lppq8ks31"))))
     (properties `((upstream-name . "PCAtools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9563,14 +11804,14 @@ dimensional mass cytometry data.")
 (define-public r-rgreat
   (package
     (name "r-rgreat")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGREAT" version))
        (sha256
         (base32
-         "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
+         "0ads9c9i8b39wvjih057zlyivj8zpsqjxf6r97yflz4sbi1jmcji"))))
     (properties `((upstream-name . "rGREAT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9591,14 +11832,14 @@ user's input and automatically retrieving results from GREAT web server.")
 (define-public r-m3c
   (package
     (name "r-m3c")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "M3C" version))
        (sha256
         (base32
-         "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
+         "17gj4haa4ywc6bmppm342jzppl3inqa94235yspikij6c098vrmc"))))
     (properties `((upstream-name . "M3C")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9624,14 +11865,14 @@ hypothesis @code{K=1}.")
 (define-public r-icens
   (package
     (name "r-icens")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Icens" version))
        (sha256
         (base32
-         "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
+         "1rzgwxx4w2bqsaz0xmkhi4w9zsxgms80xf59zg1xp1camyhaihlz"))))
     (properties `((upstream-name . "Icens")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9754,14 +11995,14 @@ generated.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.52.1")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
+         "17a00blz4kvhmsk92bp5alj9kdpy7h1id7nk4vqxakhkb2jabr20"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -9775,13 +12016,13 @@ routines.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.28.1")
+    (version "0.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh"))))
+                "0v5vxmg0a27ivgymmzfl595rcb1m3dz27r2wzbk1j97rlpwy1p4q"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -9842,14 +12083,14 @@ data manipulation and visualization.")
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-    (version "2.34.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rgraphviz" version))
        (sha256
         (base32
-         "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
+         "0d0xq1vgr4b165cn4wg7zmfjyc1d9ir4amgs196j4cgrhpmrnl8s"))))
     (properties `((upstream-name . "Rgraphviz")))
     (build-system r-build-system)
     (arguments
@@ -9880,13 +12121,13 @@ objects from the @code{graph} package.")
 (define-public r-fithic
   (package
     (name "r-fithic")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "FitHiC" version))
               (sha256
                (base32
-                "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
+                "1p8a6lis5yswaj647bjw89harlarnsxmvjzz63fn1l6gxrwhh8bx"))))
     (properties `((upstream-name . "FitHiC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9906,13 +12147,13 @@ assays such as Hi-C.")
 (define-public r-hitc
   (package
     (name "r-hitc")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "HiTC" version))
               (sha256
                (base32
-                "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
+                "0s3kfqs3zlmq61hxdmxpmi9gfs9w3byckw7xzp1hrhdbsl46yvgq"))))
     (properties `((upstream-name . "HiTC")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9935,27 +12176,16 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
+         "1718hplz5qlbwxwb87509bl7lir9kilvn1s7p2haz551pg48zvrc"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-linking
-           (lambda _
-             (substitute* "src/Makevars"
-               ;; This is to avoid having a plain directory on the list of
-               ;; libraries to link.
-               (("\\(RHDF5LIB_LIBS\\)" match)
-                (string-append match "/libhdf5.a")))
-             #t)))))
     (inputs
      `(("zlib" ,zlib)))
     (propagated-inputs
@@ -9964,6 +12194,7 @@ provided.")
        ("r-iranges" ,r-iranges)
        ("r-matrix" ,r-matrix)
        ("r-rhdf5" ,r-rhdf5)
+       ("r-rhdf5filters" ,r-rhdf5filters)
        ("r-rhdf5lib" ,r-rhdf5lib)
        ("r-s4vectors" ,r-s4vectors)))
     (home-page "https://bioconductor.org/packages/HDF5Array")
@@ -9976,22 +12207,21 @@ block processing.")
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.12.1")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
+         "1ypqmd4nz4hxlb2qsay7f5784dqdjhc3b19pckzkhb65bfycdn87"))
        (modules '((guix build utils)))
        (snippet
         '(begin
            ;; Delete bundled binaries
            (delete-file-recursively "src/wininclude/")
-           (delete-file-recursively "src/winlib-4.9.3/")
            (delete-file-recursively "src/winlib-8.3.0/")
-           (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
+           (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")
            #t))))
     (properties `((upstream-name . "Rhdf5lib")))
     (build-system r-build-system)
@@ -10003,7 +12233,9 @@ block processing.")
              (for-each delete-file '("configure" "configure.ac"))
              ;; Do not make other packages link with the proprietary libsz.
              (substitute* "R/zzz.R"
-               ((" \"%s/libsz.a\"") ""))
+               ((" \"%s/libsz.a\"") "")
+               (("patharch, .getDynamicLinks")
+                ".getDynamicLinks"))
              (with-directory-excursion "src"
                (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
                (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
@@ -10042,12 +12274,10 @@ block processing.")
                                  (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
                  ;; szip is non-free software
                  (("cp \"\\$\\{SZIP_LIB\\}.*") "")
-                 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
-             #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
+                 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
     (propagated-inputs
-     `(("hdf5" ,hdf5-1.10)))
+     `(("hdf5" ,hdf5-1.10)
+       ("zlib" ,zlib)))
     (native-inputs
      `(("hdf5-source" ,(package-source hdf5-1.10))
        ("r-knitr" ,r-knitr)))
@@ -10060,19 +12290,20 @@ packages.")
 (define-public r-beachmat
   (package
     (name "r-beachmat")
-    (version "2.6.4")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "beachmat" version))
        (sha256
         (base32
-         "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
+         "16p6shab4y8sy1adn4qr05ysvwmvs9idliccixafvx9icv5sla86"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-delayedarray" ,r-delayedarray)
-       ("r-matrix" ,r-matrix)))
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/beachmat")
@@ -10088,13 +12319,13 @@ matrices.")
 (define-public r-cner
   (package
     (name "r-cner")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CNEr" version))
        (sha256
-        (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
+        (base32 "13w0gsfm7k29dp5nb0c9sb2ix506ph6dixsjis6xxcz6acq7lg2k"))))
     (properties `((upstream-name . "CNEr")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -10136,14 +12367,14 @@ advanced visualization of sets of conserved noncoding elements.")
 (define-public r-tfbstools
   (package
     (name "r-tfbstools")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TFBSTools" version))
        (sha256
         (base32
-         "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
+         "1avgjv2nyr28cla0z9dvh3v0hr1f561sz2as1k53a42irbjk0var"))))
     (properties `((upstream-name . "TFBSTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10182,14 +12413,14 @@ provides a wrapper of de novo motif discovery software.")
 (define-public r-motifmatchr
   (package
     (name "r-motifmatchr")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifmatchr" version))
        (sha256
         (base32
-         "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z"))))
+         "1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm"))))
     (properties `((upstream-name . "motifmatchr")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10216,13 +12447,13 @@ This package wraps C++ code from the MOODS motif calling library.")
 (define-public r-chromvar
   (package
     (name "r-chromvar")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromVAR" version))
        (sha256
-        (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819"))))
+        (base32 "1birmwvcvl2hb5ygbsb3wvbdfayqqs53j1bks46cbkq7ybigfyar"))))
     (properties `((upstream-name . "chromVAR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10263,19 +12494,21 @@ sequence (@code{DNAse-seq}) experiments.")
 (define-public r-singlecellexperiment
   (package
     (name "r-singlecellexperiment")
-    (version "1.12.0")
+    (version "1.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleCellExperiment" version))
        (sha256
         (base32
-         "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
+         "1bwdhx0ss0s8f4xdgwd7x48apn849x4dyb5hbyglcz31r5vh1qgz"))))
     (properties
      `((upstream-name . "SingleCellExperiment")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-genomicranges" ,r-genomicranges)
        ("r-s4vectors" ,r-s4vectors)
        ("r-summarizedexperiment" ,r-summarizedexperiment)))
     (native-inputs
@@ -10292,14 +12525,14 @@ libraries.")
 (define-public r-scuttle
   (package
     (name "r-scuttle")
-    (version "1.0.4")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scuttle" version))
        (sha256
         (base32
-         "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
+         "1vxmgm52n5z2m1a7d4c5ajp5d35rdq7j3hln9qn7188zk9ijjsz5"))))
     (properties `((upstream-name . "scuttle")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10327,16 +12560,17 @@ of other packages.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.18.6")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609"))))
+                "0rppbd0mfyi41wb56i499mk3nj2ljhgnv3bv0k2p31bngvmb03j5"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biocgenerics" ,r-biocgenerics)
        ("r-biocneighbors" ,r-biocneighbors)
        ("r-biocparallel" ,r-biocparallel)
        ("r-biocsingular" ,r-biocsingular)
@@ -10346,7 +12580,9 @@ of other packages.")
        ("r-ggplot2" ,r-ggplot2)
        ("r-gridextra" ,r-gridextra)
        ("r-matrix" ,r-matrix)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rlang" ,r-rlang)
+       ("r-rtsne" ,r-rtsne)
        ("r-s4vectors" ,r-s4vectors)
        ("r-scuttle" ,r-scuttle)
        ("r-singlecellexperiment" ,r-singlecellexperiment)
@@ -10364,20 +12600,19 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.18.7")
+    (version "1.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "0hsr58b7xj2cqdkyjdpzyifg5wrl1lbylq2h91zbjh5861qjv2n4"))))
+         "0ilzp6ngw9pq88gk79iic2zxfh5jaic6lnq3xfwc9a269bjylff0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
        ("r-bh" ,r-bh)
        ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocneighbors" ,r-biocneighbors)
        ("r-biocparallel" ,r-biocparallel)
        ("r-biocsingular" ,r-biocsingular)
        ("r-bluster" ,r-bluster)
@@ -10388,6 +12623,7 @@ quality control.")
        ("r-igraph" ,r-igraph)
        ("r-limma" ,r-limma)
        ("r-matrix" ,r-matrix)
+       ("r-metapod" ,r-metapod)
        ("r-rcpp" ,r-rcpp)
        ("r-s4vectors" ,r-s4vectors)
        ("r-scuttle" ,r-scuttle)
@@ -10407,14 +12643,14 @@ variable and significantly correlated genes.")
 (define-public r-sparsematrixstats
   (package
     (name "r-sparsematrixstats")
-    (version "1.2.1")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sparseMatrixStats" version))
        (sha256
         (base32
-         "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
+         "0ilspddfkqpnf2lng9jjs2ahv6vlc6sap69fzkcw314rha59kncr"))))
     (properties
      `((upstream-name . "sparseMatrixStats")))
     (build-system r-build-system)
@@ -10435,21 +12671,19 @@ data in the column sparse format.")
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.12.3")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
+         "02r68rzmc54m353fpw5ampyv26i5622bc7iihfqlpy6p3033lpqk"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-delayedarray" ,r-delayedarray)
-       ("r-hdf5array" ,r-hdf5array)
+     `(("r-delayedarray" ,r-delayedarray)
        ("r-iranges" ,r-iranges)
        ("r-matrix" ,r-matrix)
        ("r-matrixgenerics" ,r-matrixgenerics)
@@ -10473,18 +12707,19 @@ memory usage and processing time is minimized.")
 (define-public r-mscoreutils
   (package
     (name "r-mscoreutils")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsCoreUtils" version))
        (sha256
         (base32
-         "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
+         "13g8a726vsyjs6m1kd42vf8avdnmhykxhl6z3j2njzkp2jg17pd8"))))
     (properties `((upstream-name . "MsCoreUtils")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-mass" ,r-mass)
+     `(("r-clue" ,r-clue)
+       ("r-mass" ,r-mass)
        ("r-rcpp" ,r-rcpp)
        ("r-s4vectors" ,r-s4vectors)))
     (native-inputs
@@ -10504,21 +12739,19 @@ within the R for Mass Spectrometry packages.")
 (define-public r-biocio
   (package
     (name "r-biocio")
-    (version "1.0.1")
+    (version "1.2.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "BiocIO" version))
         (sha256
           (base32
-            "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
+            "0skwnpxl6fkqihidpqrfzzh7b05x11j6jwkiinmhggmv0ggjb5ph"))))
     (properties `((upstream-name . "BiocIO")))
     (build-system r-build-system)
     (propagated-inputs
-      `(("r-biocgenerics" ,r-biocgenerics)
-        ("r-genomicranges" ,r-genomicranges)
-        ("r-rcurl" ,r-rcurl)
-        ("r-s4vectors" ,r-s4vectors)))
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/BiocIO")
@@ -10540,14 +12773,14 @@ as well as local access.  Developers can register a file extension, e.g.,
 (define-public r-msmseda
   (package
     (name "r-msmseda")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsEDA" version))
        (sha256
         (base32
-         "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
+         "0555a3riyp781mlffmnf93igfq8vl8wjk51pa9qb48qkdn6y8pfc"))))
     (properties `((upstream-name . "msmsEDA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10566,14 +12799,14 @@ experiments, and visualize de influence of the involved factors.")
 (define-public r-msmstests
   (package
     (name "r-msmstests")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsTests" version))
        (sha256
         (base32
-         "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
+         "11vhy1l6za73dpdj85q4ksaghgd8vb2h8v9iirmsn2vpajqrvgjh"))))
     (properties `((upstream-name . "msmsTests")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10598,14 +12831,14 @@ relevant, and the minimum expression of the most abundant condition.")
 (define-public r-catalyst
   (package
     (name "r-catalyst")
-    (version "1.14.1")
+    (version "1.16.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "CATALYST" version))
         (sha256
           (base32
-            "04b5kcvkfiw4ina11x3qf5kwrb7056zihm7xp1919bqm8k7nl3mn"))))
+            "1lzi3wylx94k3gmfw5lsqh3cvg485ik3n5xd51jllczgavwvki16"))))
     (properties `((upstream-name . "CATALYST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10656,14 +12889,14 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
 (define-public r-erma
   (package
     (name "r-erma")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "erma" version))
        (sha256
         (base32
-         "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
+         "02a9702sasgighwb0f9ii8n30ngfx1hjnppaay1f5zsigr8vqalz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10696,14 +12929,14 @@ by Ernst and Kellis.")
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
+         "0k3dxacrwgyrkvm7ggc2s1s1pbfs6c0a7ngykkj7jnc73czvnilx"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -10864,14 +13097,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.34.1")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1"))))
+         "19vjf4sdz5sxbcdilsqx7m57fq5a8xnxjf354zx2l5mgjrkzkk3h"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10913,17 +13146,18 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
+         "0109cxsviq1sk5hfwkjzd0y1kpm934287asjjd0j8jhh4b0ah2b2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationhub" ,r-annotationhub)
        ("r-biocfilecache" ,r-biocfilecache)
        ("r-biostrings" ,r-biostrings)
        ("r-genomeinfodb" ,r-genomeinfodb)
@@ -10946,18 +13180,19 @@ EMBL-EBI GWAS catalog.")
 (define-public r-kegggraph
   (package
     (name "r-kegggraph")
-    (version "1.50.0")
+    (version "1.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGgraph" version))
        (sha256
-        (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
+        (base32 "0zxdph5hzr3kzj2g1mjqpiviwa189a5sq4bw7wiry6r79fdnklqs"))))
     (properties `((upstream-name . "KEGGgraph")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-graph" ,r-graph)
        ("r-rcurl" ,r-rcurl)
+       ("r-rgraphviz" ,r-rgraphviz)
        ("r-xml" ,r-xml)))
     (home-page "https://bioconductor.org/packages/KEGGgraph")
     (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
@@ -10972,14 +13207,14 @@ functionalities including parsing, graph operation, visualization and etc.")
 (define-public r-ldblock
   (package
     (name "r-ldblock")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ldblock" version))
        (sha256
         (base32
-         "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
+         "075jncvfbn3lydg0jvfhnv5025mnw79saa0k557vpcwdvs9y4p0c"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
@@ -11069,16 +13304,42 @@ network models for a given data set, where these models are used to identify
 statistical dependencies in messy, complex data.")
     (license license:gpl2+)))
 
+;; This is a CRAN package, but it depends on r-rsamtools, which is a
+;; Bioconductor package.
+(define-public r-spp
+  (package
+    (name "r-spp")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "spp" version))
+              (sha256
+               (base32
+                "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-catools" ,r-catools)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rsamtools" ,r-rsamtools)))
+    (home-page "https://cran.r-project.org/web/packages/spp/")
+    (synopsis "ChIP-Seq processing pipeline")
+    (description "This package provides tools for analysis of ChIP-seq and
+other functional sequencing data.")
+    (license license:gpl2)))
+
 (define-public r-pathview
   (package
     (name "r-pathview")
-    (version "1.30.1")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pathview" version))
        (sha256
-        (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
+        (base32 "1fank0qavv9ikmzxvms8mky2wbzny02rfqkvsqzma26r3vl4r1g1"))))
     (properties `((upstream-name . "pathview")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11106,14 +13367,14 @@ large-scale and fully automated analysis.")
 (define-public r-snpstats
   (package
     (name "r-snpstats")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "snpStats" version))
        (sha256
         (base32
-         "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
+         "11vvih5y9kvyjfp2navkfpp4xiyfgwlv4r0x3p52hkj92pc2pg3g"))))
     (properties `((upstream-name . "snpStats")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -11133,14 +13394,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
 (define-public r-chromstar
   (package
     (name "r-chromstar")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromstaR" version))
        (sha256
         (base32
-         "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1"))))
+         "09cqzylci4x4i7wn4ckcqhdlljbzfrp08wdvkkc5vrdldnj9pq5h"))))
     (properties `((upstream-name . "chromstaR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11171,14 +13432,14 @@ analyses.")
 (define-public r-guitar
   (package
     (name "r-guitar")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Guitar" version))
        (sha256
         (base32
-         "0lvfrpgrvmrz4f4qmsii70hw10h72zh1g1alv2sf6a6ixhndm0mz"))))
+         "1q4m6c5181dw12lvdp324jlk78c9jgcsg6b9hk87zjadp6j0gfr6"))))
     (properties `((upstream-name . "Guitar")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11203,13 +13464,13 @@ starting site, start codon, stop codon and transcription ending site.")
 (define-public r-sushi
   (package
     (name "r-sushi")
-    (version "1.28.0")
+    (version "1.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Sushi" version))
               (sha256
                (base32
-                "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
+                "1m5l0nflhcynb3gz7b8qzvknb0s6xhds8z1yl3mbv8ic9qn2knv4"))))
     (properties `((upstream-name . "Sushi")))
     (build-system r-build-system)
     (propagated-inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fc2fc867ac..64fc6173db 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -122,6 +122,7 @@
   #:use-module (gnu packages popt)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-compression)
   #:use-module (gnu packages python-science)
@@ -310,6 +311,37 @@ instance, it implements several methods to assess contig-wise read coverage.")
 BAM files.")
     (license license:expat)))
 
+(define-public bamutils
+  (package
+    (name "bamutils")
+    (version "1.0.13")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append
+                "https://genome.sph.umich.edu/w/images/7/70/"
+                "BamUtilLibStatGen." version ".tgz"))
+              (sha256
+               (base32
+                "0asr1kmjbr3cyf4hkg865y8c2s30v87xvws4q6c8pyfi6wfd1h8n"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; There are no tests.
+       #:make-flags `("USER_WARNINGS=-std=gnu++98"
+                      ,(string-append "INSTALLDIR="
+                                      (assoc-ref %outputs "out") "/bin"))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://genome.sph.umich.edu/wiki/BamUtil")
+    (synopsis "Programs for working on SAM/BAM files")
+    (description "This package provides several programs that perform
+operations on SAM/BAM files.  All of these programs are built into a
+single executable called @code{bam}.")
+    (license license:gpl3+)))
+
 (define-public bcftools
   (package
     (name "bcftools")
@@ -830,6 +862,30 @@ input/output delimiter.  When the new functionality is not used, bioawk is
 intended to behave exactly the same as the original BWK awk.")
     (license license:x11)))
 
+(define-public python-htsget
+  (package
+   (name "python-htsget")
+   (version "0.2.5")
+   (source (origin
+            (method url-fetch)
+            (uri (pypi-uri "htsget" version))
+            (sha256
+             (base32
+              "0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk"))))
+   (build-system python-build-system)
+   (native-inputs
+    `(("python-setuptools-scm" ,python-setuptools-scm)))
+   (propagated-inputs
+    `(("python-humanize" ,python-humanize)
+      ("python-requests" ,python-requests)
+      ("python-six" ,python-six)))
+   (home-page "https://pypi.org/project/htsget/")
+   (synopsis "Python API and command line interface for the GA4GH htsget API")
+   (description "This package is a client implementation of the GA4GH htsget
+protocol.  It provides a simple and reliable way to retrieve genomic data from
+servers supporting the protocol.")
+   (license license:asl2.0)))
+
 (define-public python-pybedtools
   (package
     (name "python-pybedtools")
@@ -1942,6 +1998,45 @@ multiple sequence alignments.")
 (define-public python2-bx-python
   (package-with-python2 python-bx-python))
 
+(define-public python-pyega3
+  (package
+    (name "python-pyega3")
+    (version "3.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "pyega3" version))
+              (sha256
+               (base32
+                "1k736in8g27rarx65ym9xk50x53zjg75h37bb8ljynxv04rypx2q"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ; The tests require network access.
+    (native-inputs
+     `(("python-psutil" ,python-psutil)
+       ("python-htsget" ,python-htsget)))
+    (propagated-inputs
+     `(("python-requests" ,python-requests)
+       ("python-tqdm" ,python-tqdm)
+       ("python-urllib3" ,python-urllib3)
+       ("python-responses" ,python-responses)))
+    (home-page "https://github.com/EGA-archive/ega-download-client")
+    (synopsis "Python client for EGA")
+    (description "This package is a python-based tool for viewing and
+downloading files from authorized EGA datasets.  It uses the EGA data API and
+has several key features:
+@itemize
+@item Files are transferred over secure https connections and received
+  unencrypted, so no need for decryption after download.
+@item Downloads resume from where they left off in the event that the
+  connection is interrupted.
+@item Supports file segmenting and parallelized download of segments,
+  improving overall performance.
+@item After download completes, file integrity is verified using checksums.
+@item Implements the GA4GH-compliant htsget protocol for download of genomic
+  ranges for data files with accompanying index files.
+@end itemize\n")
+    (license license:asl2.0)))
+
 (define-public python-pysam
   (package
     (name "python-pysam")
@@ -6065,6 +6160,46 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
       ;; 2. MD5 implementation - RSA Data Security, RFC 1321
       (license (list license:gpl2+ license:public-domain)))))
 
+(define-public mosaicatcher
+  (package
+    (name "mosaicatcher")
+    (version "0.3.1")
+    (source (origin
+              ;; There are no release tarballs nor tags.
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/friendsofstrandseq/mosaicatcher")
+                    (commit (string-append version "-dev"))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd"))
+              (patches (search-patches "mosaicatcher-unbundle-htslib.patch"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #false ; there are no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'chdir
+           (lambda _ (chdir "src")))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((target (assoc-ref outputs "out"))
+                    (bin (string-append target "/bin"))
+                    (share (string-append target "/share/mosaicatcher")))
+               (install-file "mosaic" bin)
+               (mkdir-p share)
+               (copy-recursively "../R" share)))))))
+    (inputs
+     `(("boost" ,boost)
+       ("htslib" ,htslib)))
+    (home-page "https://github.com/friendsofstrandseq/mosaicatcher")
+    (synopsis "Count and classify Strand-seq reads")
+    (description
+     "Mosaicatcher counts Strand-seq reads and classifies strand states of
+each chromosome in each cell using a Hidden Markov Model.")
+    (license license:expat)))
+
 (define-public ngs-sdk
   (package
     (name "ngs-sdk")
@@ -7790,409 +7925,54 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-genomicalignments
-  (package
-    (name "r-genomicalignments")
-    (version "1.26.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "GenomicAlignments" version))
-              (sha256
-               (base32
-                "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
-    (properties
-     `((upstream-name . "GenomicAlignments")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (home-page "https://bioconductor.org/packages/GenomicAlignments")
-    (synopsis "Representation and manipulation of short genomic alignments")
-    (description
-     "This package provides efficient containers for storing and manipulating
-short genomic alignments (typically obtained by aligning short reads to a
-reference genome).  This includes read counting, computing the coverage,
-junction detection, and working with the nucleotide content of the
-alignments.")
-    (license license:artistic2.0)))
-
-(define-public r-rtracklayer
-  (package
-    (name "r-rtracklayer")
-    (version "1.50.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "rtracklayer" version))
-              (sha256
-               (base32
-                "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-system-zlib
-           (lambda _
-             (substitute* "DESCRIPTION"
-               ((" zlibbioc,") ""))
-             (substitute* "NAMESPACE"
-               (("import\\(zlibbioc\\)") ""))
-             #t)))))
-    (native-inputs
-     `(("pkg-config" ,pkg-config)))
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xml" ,r-xml)
-       ("r-xvector" ,r-xvector)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (home-page "https://bioconductor.org/packages/rtracklayer")
-    (synopsis "R interface to genome browsers and their annotation tracks")
-    (description
-     "rtracklayer is an extensible framework for interacting with multiple
-genome browsers (currently UCSC built-in) and manipulating annotation tracks
-in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
-built-in).  The user may export/import tracks to/from the supported browsers,
-as well as query and modify the browser state, such as the current viewport.")
-    (license license:artistic2.0)))
-
-(define-public r-genomicfeatures
-  (package
-    (name "r-genomicfeatures")
-    (version "1.42.3")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "GenomicFeatures" version))
-              (sha256
-               (base32
-                "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))
-    (properties
-     `((upstream-name . "GenomicFeatures")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/GenomicFeatures")
-    (synopsis "Tools for working with transcript centric annotations")
-    (description
-     "This package provides a set of tools and methods for making and
-manipulating transcript centric annotations.  With these tools the user can
-easily download the genomic locations of the transcripts, exons and cds of a
-given organism, from either the UCSC Genome Browser or a BioMart
-database (more sources will be supported in the future).  This information is
-then stored in a local database that keeps track of the relationship between
-transcripts, exons, cds and genes.  Flexible methods are provided for
-extracting the desired features in a convenient format.")
-    (license license:artistic2.0)))
-
-(define-public r-go-db
-  (package
-    (name "r-go-db")
-    (version "3.7.0")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/GO.db_"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
-    (properties
-     `((upstream-name . "GO.db")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
-    (home-page "https://bioconductor.org/packages/GO.db")
-    (synopsis "Annotation maps describing the entire Gene Ontology")
-    (description
-     "The purpose of this GO.db annotation package is to provide detailed
-information about the latest version of the Gene Ontologies.")
-    (license license:artistic2.0)))
-
-(define-public r-topgo
-  (package
-    (name "r-topgo")
-    (version "2.42.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "topGO" version))
-              (sha256
-               (base32
-                "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))
-    (properties
-     `((upstream-name . "topGO")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-dbi" ,r-dbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-go-db" ,r-go-db)
-       ("r-graph" ,r-graph)
-       ("r-lattice" ,r-lattice)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-sparsem" ,r-sparsem)))
-    (home-page "https://bioconductor.org/packages/topGO")
-    (synopsis "Enrichment analysis for gene ontology")
-    (description
-     "The topGO package provides tools for testing @dfn{gene ontology} (GO)
-terms while accounting for the topology of the GO graph.  Different test
-statistics and different methods for eliminating local similarities and
-dependencies between GO terms can be implemented and applied.")
-    ;; Any version of the LGPL applies.
-    (license license:lgpl2.1+)))
-
-(define-public r-bsgenome
-  (package
-    (name "r-bsgenome")
-    (version "1.58.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "BSgenome" version))
-              (sha256
-               (base32
-                "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
-    (properties
-     `((upstream-name . "BSgenome")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (home-page "https://bioconductor.org/packages/BSgenome")
-    (synopsis "Infrastructure for Biostrings-based genome data packages")
-    (description
-     "This package provides infrastructure shared by all Biostrings-based
-genome data packages and support for efficient SNP representation.")
-    (license license:artistic2.0)))
-
-(define-public r-impute
-  (package
-    (name "r-impute")
-    (version "1.64.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "impute" version))
-              (sha256
-               (base32
-                "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))
-    (native-inputs
-     `(("gfortran" ,gfortran)))
-    (build-system r-build-system)
-    (home-page "https://bioconductor.org/packages/impute")
-    (synopsis "Imputation for microarray data")
-    (description
-     "This package provides a function to impute missing gene expression
-microarray data, using nearest neighbor averaging.")
-    (license license:gpl2+)))
-
-(define-public r-seqpattern
-  (package
-    (name "r-seqpattern")
-    (version "1.22.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "seqPattern" version))
-              (sha256
-               (base32
-                "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq"))))
-    (properties
-     `((upstream-name . "seqPattern")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-plotrix" ,r-plotrix)))
-    (home-page "https://bioconductor.org/packages/seqPattern")
-    (synopsis "Visualising oligonucleotide patterns and motif occurrences")
-    (description
-     "This package provides tools to visualize oligonucleotide patterns and
-sequence motif occurrences across a large set of sequences centred at a common
-reference point and sorted by a user defined feature.")
-    (license license:gpl3+)))
-
-(define-public r-genomation
-  (package
-    (name "r-genomation")
-    (version "1.22.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "genomation" version))
-              (sha256
-               (base32
-                "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-data-table" ,r-data-table)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridbase" ,r-gridbase)
-       ("r-impute" ,r-impute)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-plotrix" ,r-plotrix)
-       ("r-plyr" ,r-plyr)
-       ("r-rcpp" ,r-rcpp)
-       ("r-readr" ,r-readr)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-runit" ,r-runit)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-seqpattern" ,r-seqpattern)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
-    (synopsis "Summary, annotation and visualization of genomic data")
-    (description
-     "This package provides a package for summary and annotation of genomic
-intervals.  Users can visualize and quantify genomic intervals over
-pre-defined functional regions, such as promoters, exons, introns, etc.  The
-genomic intervals represent regions with a defined chromosome position, which
-may be associated with a score, such as aligned reads from HT-seq experiments,
-TF binding sites, methylation scores, etc.  The package can use any tabular
-genomic feature data as long as it has minimal information on the locations of
-genomic intervals.  In addition, it can use BAM or BigWig files as input.")
-    (license license:artistic2.0)))
-
-(define-public r-genomationdata
-  (package
-    (name "r-genomationdata")
-    (version "1.22.0")
-    (source (origin
-              (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://bioconductor.org/packages/"
-                                  "release/data/experiment/src/contrib/"
-                                  "genomationData_" version ".tar.gz"))
-              (sha256
-               (base32
-                "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
-    (build-system r-build-system)
-    ;; As this package provides little more than large data files, it doesn't
-    ;; make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
-    (synopsis "Experimental data for use with the genomation package")
-    (description
-     "This package contains experimental genetic data for use with the
-genomation package.  Included are Chip Seq, Methylation and Cage data,
-downloaded from Encode.")
-    (license license:gpl3+)))
-
-(define-public r-seqlogo
-  (package
-    (name "r-seqlogo")
-    (version "1.56.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "seqLogo" version))
-       (sha256
-        (base32
-         "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1"))))
-    (properties `((upstream-name . "seqLogo")))
-    (build-system r-build-system)
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/seqLogo")
-    (synopsis "Sequence logos for DNA sequence alignments")
-    (description
-     "seqLogo takes the position weight matrix of a DNA sequence motif and
-plots the corresponding sequence logo as introduced by Schneider and
-Stephens (1990).")
-    (license license:lgpl2.0+)))
-
-(define-public r-motifrg
-  (package
-    (name "r-motifrg")
-    (version "1.31.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "motifRG" version))
-       (sha256
-        (base32
-         "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
-    (properties `((upstream-name . "motifRG")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-iranges" ,r-iranges)
-       ("r-seqlogo" ,r-seqlogo)
-       ("r-xvector" ,r-xvector)))
-    (home-page "https://bioconductor.org/packages/motifRG")
-    (synopsis "Discover motifs in high throughput sequencing data")
-    (description
-     "This package provides tools for discriminative motif discovery in high
-throughput genetic sequencing data sets using regression methods.")
-    (license license:artistic2.0)))
-
-(define-public r-zlibbioc
-  (package
-    (name "r-zlibbioc")
-    (version "1.36.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "zlibbioc" version))
-              (sha256
-               (base32
-                "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg"))))
-    (properties
-     `((upstream-name . "zlibbioc")))
-    (build-system r-build-system)
-    (home-page "https://bioconductor.org/packages/zlibbioc")
-    (synopsis "Provider for zlib-1.2.5 to R packages")
-    (description "This package uses the source code of zlib-1.2.5 to create
-libraries for systems that do not have these available via other means.")
-    (license license:artistic2.0)))
+(define-public r-phantompeakqualtools
+  (let ((commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42")
+        (revision "1"))
+    (package
+      (name "r-phantompeakqualtools")
+      (version (git-version "1.2.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/kundajelab/phantompeakqualtools")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f ; There are no tests.
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (delete 'build)
+           (replace 'install
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let ((script (string-append (assoc-ref outputs "out")
+                                            "/share/scripts")))
+                 (install-file "run_spp.R" script)))))))
+      (inputs
+       `(("r" ,r-minimal)))
+      (propagated-inputs
+       `(("r-catools" ,r-catools)
+         ("r-snow" ,r-snow)
+         ("r-snowfall" ,r-snowfall)
+         ("r-bitops" ,r-bitops)
+         ("r-rsamtools" ,r-rsamtools)
+         ("r-spp" ,r-spp)
+         ("gawk" ,gawk)
+         ("samtools" ,samtools)
+         ("boost" ,boost)
+         ("gzip" ,gzip)))
+      (home-page "https://github.com/kundajelab/phantompeakqualtools")
+      (synopsis "Informative enrichment for ChIP-seq data")
+      (description "This package computes informative enrichment and quality
+measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.  It can also be
+used to obtain robust estimates of the predominant fragment length or
+characteristic tag shift values in these assays.")
+      (license license:bsd-3))))
 
 (define-public r-r4rna
   (package
@@ -8217,116 +7997,6 @@ libraries for systems that do not have these available via other means.")
 secondary structure and comparative analysis in R.")
     (license license:gpl3+)))
 
-(define-public r-rhtslib
-  (package
-    (name "r-rhtslib")
-    (version "1.22.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "Rhtslib" version))
-       (sha256
-        (base32
-         "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
-    (properties `((upstream-name . "Rhtslib")))
-    (build-system r-build-system)
-    ;; Without this a temporary directory ends up in the Rhtslib.so binary,
-    ;; which makes R abort the build.
-    (arguments '(#:configure-flags '("--no-staged-install")))
-    (propagated-inputs
-     `(("curl" ,curl)
-       ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (native-inputs
-     `(("pkg-config" ,pkg-config)
-       ("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/nhayden/Rhtslib")
-    (synopsis "High-throughput sequencing library as an R package")
-    (description
-     "This package provides the HTSlib C library for high-throughput
-nucleotide sequence analysis.  The package is primarily useful to developers
-of other R packages who wish to make use of HTSlib.")
-    (license license:lgpl2.0+)))
-
-(define-public r-bamsignals
-  (package
-    (name "r-bamsignals")
-    (version "1.22.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "bamsignals" version))
-       (sha256
-        (base32
-         "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/bamsignals")
-    (synopsis "Extract read count signals from bam files")
-    (description
-     "This package efficiently obtains count vectors from indexed bam
-files.  It counts the number of nucleotide sequence reads in given genomic
-ranges and it computes reads profiles and coverage profiles.  It also handles
-paired-end data.")
-    (license license:gpl2+)))
-
-(define-public r-rcas
-  (package
-    (name "r-rcas")
-    (version "1.16.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "RCAS" version))
-              (sha256
-               (base32
-                "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m"))))
-    (properties `((upstream-name . "RCAS")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-cowplot" ,r-cowplot)
-       ("r-data-table" ,r-data-table)
-       ("r-dt" ,r-dt)
-       ("r-genomation" ,r-genomation)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggseqlogo" ,r-ggseqlogo)
-       ("r-gprofiler2" ,r-gprofiler2)
-       ("r-iranges" ,r-iranges)
-       ("r-pbapply" ,r-pbapply)
-       ("r-pheatmap" ,r-pheatmap)
-       ("r-plotly" ,r-plotly)
-       ("r-plotrix" ,r-plotrix)
-       ("r-proxy" ,r-proxy)
-       ("r-ranger" ,r-ranger)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("r-s4vectors" ,r-s4vectors)
-       ("pandoc" ,pandoc)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (synopsis "RNA-centric annotation system")
-    (description
-     "RCAS aims to be a standalone RNA-centric annotation system that provides
-intuitive reports and publication-ready graphics.  This package provides the R
-library implementing most of the pipeline's features.")
-    (home-page "https://github.com/BIMSBbioinfo/RCAS")
-    (license license:artistic2.0)))
-
 (define-public rcas-web
   (package
     (name "rcas-web")
@@ -8378,64 +8048,19 @@ library implementing most of the pipeline's features.")
 @dfn{RNA-centric annotation system} (RCAS).")
     (license license:agpl3+)))
 
-(define-public r-mutationalpatterns
-  (package
-    (name "r-mutationalpatterns")
-    (version "3.0.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "MutationalPatterns" version))
-       (sha256
-        (base32
-         "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ;; These two packages are suggested packages
-       ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-cowplot" ,r-cowplot)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggalluvial" ,r-ggalluvial)
-       ("r-ggdendro" ,r-ggdendro)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-magrittr" ,r-magrittr)
-       ("r-nmf" ,r-nmf)
-       ("r-pracma" ,r-pracma)
-       ("r-purrr" ,r-purrr)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)
-       ("r-variantannotation" ,r-variantannotation)))
-    (home-page "https://bioconductor.org/packages/MutationalPatterns/")
-    (synopsis "Extract and visualize mutational patterns in genomic data")
-    (description "This package provides an extensive toolset for the
-characterization and visualization of a wide range of mutational patterns
-in SNV base substitution data.")
-    (license license:expat)))
-
 (define-public r-chipkernels
   (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
         (revision "1"))
     (package
       (name "r-chipkernels")
-      (version (string-append "1.1-" revision "." (string-take commit 9)))
+      (version (git-version "1.1" revision commit))
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
                (url "https://github.com/ManuSetty/ChIPKernels")
                (commit commit)))
-         (file-name (string-append name "-" version))
+         (file-name (git-file-name name version))
          (sha256
           (base32
            "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
@@ -8490,121 +8115,6 @@ bound and non bound genomic regions to accurately identify transcription
 factors bound at the specific regions.")
     (license license:gpl2+)))
 
-(define-public r-tximport
-  (package
-    (name "r-tximport")
-    (version "1.18.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "tximport" version))
-              (sha256
-               (base32
-                "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/tximport")
-    (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
-    (description
-     "This package provides tools to import transcript-level abundance,
-estimated counts and transcript lengths, and to summarize them into matrices
-for use with downstream gene-level analysis packages.  Average transcript
-length, weighted by sample-specific transcript abundance estimates, is
-provided as a matrix which can be used as an offset for different expression
-of gene-level counts.")
-    (license license:gpl2+)))
-
-(define-public r-rhdf5filters
-  (package
-    (name "r-rhdf5filters")
-    (version "1.2.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "rhdf5filters" version))
-       (sha256
-        (base32
-         "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz"))))
-    (properties `((upstream-name . "rhdf5filters")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-rhdf5lib" ,r-rhdf5lib)))
-    (inputs
-     `(("zlib" ,zlib)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/grimbough/rhdf5filters")
-    (synopsis "HDF5 compression filters")
-    (description
-     "This package provides a collection of compression filters for use with
-HDF5 datasets.")
-    (license license:bsd-2)))
-
-(define-public r-rhdf5
-  (package
-    (name "r-rhdf5")
-    (version "2.34.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "rhdf5" version))
-              (sha256
-               (base32
-                "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-linking
-           (lambda _
-             (substitute* "src/Makevars"
-               ;; This is to avoid having a plain directory on the list of
-               ;; libraries to link.
-               (("\\(RHDF5_LIBS\\)" match)
-                (string-append match "/libhdf5.a")))
-             #t)))))
-    (propagated-inputs
-     `(("r-rhdf5filters" ,r-rhdf5filters)
-       ("r-rhdf5lib" ,r-rhdf5lib)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/rhdf5")
-    (synopsis "HDF5 interface to R")
-    (description
-     "This R/Bioconductor package provides an interface between HDF5 and R.
-HDF5's main features are the ability to store and access very large and/or
-complex datasets and a wide variety of metadata on mass storage (disk) through
-a completely portable file format.  The rhdf5 package is thus suited for the
-exchange of large and/or complex datasets between R and other software
-package, and for letting R applications work on datasets that are larger than
-the available RAM.")
-    (license license:artistic2.0)))
-
-(define-public r-annotationfilter
-  (package
-    (name "r-annotationfilter")
-    (version "1.14.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "AnnotationFilter" version))
-              (sha256
-               (base32
-                "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9"))))
-    (properties
-     `((upstream-name . "AnnotationFilter")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-genomicranges" ,r-genomicranges)
-       ("r-lazyeval" ,r-lazyeval)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/Bioconductor/AnnotationFilter")
-    (synopsis "Facilities for filtering Bioconductor annotation resources")
-    (description
-     "This package provides classes and other infrastructure to implement
-filters for manipulating Bioconductor annotation resources.  The filters are
-used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
-    (license license:artistic2.0)))
-
 (define-public emboss
   (package
     (name "emboss")
@@ -8675,13 +8185,13 @@ tools for sequence analysis into a seamless whole.")
       (name "bits")
       ;; The version is 2.13.0 even though no release archives have been
       ;; published as yet.
-      (version (string-append "2.13.0-" revision "." (string-take commit 9)))
+      (version (git-version "2.13.0" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
                       (url "https://github.com/arq5x/bits")
                       (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
@@ -8721,7 +8231,7 @@ intervals (e.g. genes, sequence alignments).")
         (commit   "0466d364b71117d01e4471b74c514436cc281233"))
     (package
       (name "piranha")
-      (version (string-append "1.2.1-" revision "." (string-take commit 9)))
+      (version (git-version "1.2.1" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -8810,10 +8320,11 @@ group or two ChIP groups run under different conditions.")
     (license license:gpl3+)))
 
 (define-public filevercmp
-  (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
+  (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")
+        (revision "1"))
     (package
       (name "filevercmp")
-      (version (string-append "0-1." (string-take commit 7)))
+      (version (git-version "0" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -8927,176 +8438,6 @@ analysis, variant tools is project based and provides a whole set of tools to
 manipulate and analyze genetic variants.")
     (license license:gpl3+)))
 
-(define-public r-chipseq
-  (package
-    (name "r-chipseq")
-    (version "1.40.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "chipseq" version))
-       (sha256
-        (base32
-         "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shortread" ,r-shortread)))
-    (home-page "https://bioconductor.org/packages/chipseq")
-    (synopsis "Package for analyzing ChIPseq data")
-    (description
-     "This package provides tools for processing short read data from ChIPseq
-experiments.")
-    (license license:artistic2.0)))
-
-(define-public r-copyhelper
-  (package
-    (name "r-copyhelper")
-    (version "1.6.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://bioconductor.org/packages/release/"
-                           "data/experiment/src/contrib/CopyhelpeR_"
-                           version ".tar.gz"))
-       (sha256
-        (base32
-         "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
-    (properties `((upstream-name . "CopyhelpeR")))
-    (build-system r-build-system)
-    (home-page "https://bioconductor.org/packages/CopyhelpeR/")
-    (synopsis "Helper files for CopywriteR")
-    (description
-     "This package contains the helper files that are required to run the
-Bioconductor package CopywriteR.  It contains pre-assembled 1kb bin GC-content
-and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
-mm10.  In addition, it contains a blacklist filter to remove regions that
-display copy number variation.  Files are stored as GRanges objects from the
-GenomicRanges Bioconductor package.")
-    (license license:gpl2)))
-
-(define-public r-copywriter
-  (package
-    (name "r-copywriter")
-    (version "2.22.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "CopywriteR" version))
-       (sha256
-        (base32
-         "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f"))))
-    (properties `((upstream-name . "CopywriteR")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-chipseq" ,r-chipseq)
-       ("r-copyhelper" ,r-copyhelper)
-       ("r-data-table" ,r-data-table)
-       ("r-dnacopy" ,r-dnacopy)
-       ("r-futile-logger" ,r-futile-logger)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gtools" ,r-gtools)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://github.com/PeeperLab/CopywriteR")
-    (synopsis "Copy number information from targeted sequencing")
-    (description
-     "CopywriteR extracts DNA copy number information from targeted sequencing
-by utilizing off-target reads.  It allows for extracting uniformly distributed
-copy number information, can be used without reference, and can be applied to
-sequencing data obtained from various techniques including chromatin
-immunoprecipitation and target enrichment on small gene panels.  Thereby,
-CopywriteR constitutes a widely applicable alternative to available copy
-number detection tools.")
-    (license license:gpl2)))
-
-(define-public r-methylkit
-  (package
-    (name "r-methylkit")
-    (version "1.16.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "methylKit" version))
-              (sha256
-               (base32
-                "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))
-    (properties `((upstream-name . "methylKit")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-emdbook" ,r-emdbook)
-       ("r-fastseg" ,r-fastseg)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gtools" ,r-gtools)
-       ("r-iranges" ,r-iranges)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-limma" ,r-limma)
-       ("r-mclust" ,r-mclust)
-       ("r-mgcv" ,r-mgcv)
-       ("r-qvalue" ,r-qvalue)
-       ("r-r-utils" ,r-r-utils)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr))) ; for vignettes
-    (home-page "https://github.com/al2na/methylKit")
-    (synopsis
-     "DNA methylation analysis from high-throughput bisulfite sequencing results")
-    (description
-     "MethylKit is an R package for DNA methylation analysis and annotation
-from high-throughput bisulfite sequencing.  The package is designed to deal
-with sequencing data from @dfn{Reduced representation bisulfite
-sequencing} (RRBS) and its variants, but also target-capture methods and whole
-genome bisulfite sequencing.  It also has functions to analyze base-pair
-resolution 5hmC data from experimental protocols such as oxBS-Seq and
-TAB-Seq.")
-    (license license:artistic2.0)))
-
-(define-public r-sva
-  (package
-    (name "r-sva")
-    (version "3.38.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "sva" version))
-       (sha256
-        (base32
-         "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-edger" ,r-edger)
-       ("r-genefilter" ,r-genefilter)
-       ("r-mgcv" ,r-mgcv)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-limma" ,r-limma)))
-    (home-page "https://bioconductor.org/packages/sva")
-    (synopsis "Surrogate variable analysis")
-    (description
-     "This package contains functions for removing batch effects and other
-unwanted variation in high-throughput experiment.  It also contains functions
-for identifying and building surrogate variables for high-dimensional data
-sets.  Surrogate variables are covariates constructed directly from
-high-dimensional data like gene expression/RNA sequencing/methylation/brain
-imaging data that can be used in subsequent analyses to adjust for unknown,
-unmodeled, or latent sources of noise.")
-    (license license:artistic2.0)))
-
 (define-public r-raremetals2
   (package
     (name "r-raremetals2")
@@ -9129,807 +8470,6 @@ for analyzing gene-level association tests in meta-analyses for binary
 trait.")
     (license license:gpl3)))
 
-(define-public r-protgenerics
-  (package
-    (name "r-protgenerics")
-    (version "1.22.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ProtGenerics" version))
-       (sha256
-        (base32
-         "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz"))))
-    (properties `((upstream-name . "ProtGenerics")))
-    (build-system r-build-system)
-    (home-page "https://github.com/lgatto/ProtGenerics")
-    (synopsis "S4 generic functions for proteomics infrastructure")
-    (description
-     "This package provides S4 generic functions needed by Bioconductor
-proteomics packages.")
-    (license license:artistic2.0)))
-
-(define-public r-mzr
-  (package
-    (name "r-mzr")
-    (version "2.24.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "mzR" version))
-       (sha256
-        (base32
-         "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           (delete-file-recursively "src/boost")
-           #t))))
-    (properties `((upstream-name . "mzR")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-system-boost
-           (lambda _
-             (substitute* "src/Makevars"
-               (("\\./boost/libs.*") "")
-               ;; This is to avoid having a plain directory on the list of
-               ;; libraries to link.
-               (("\\(RHDF5_LIBS\\)" match)
-                (string-append match "/libhdf5.a"))
-               (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
-               (("\\ARCH_OBJS=" line)
-                (string-append line
-                               "\nBOOST_LIBS=-lboost_system -lboost_regex \
--lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
-             #t)))))
-    (inputs
-     `(;; Our default boost package won't work here, unfortunately, even with
-       ;; mzR version 2.24.1.
-       ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
-       ("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-ncdf4" ,r-ncdf4)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/sneumann/mzR/")
-    (synopsis "Parser for mass spectrometry data files")
-    (description
-     "The mzR package provides a unified API to the common file formats and
-parsers available for mass spectrometry data.  It comes with a wrapper for the
-ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
-The package contains the original code written by the ISB, and a subset of the
-proteowizard library for mzML and mzIdentML.  The netCDF reading code has
-previously been used in XCMS.")
-    (license license:artistic2.0)))
-
-(define-public r-affyio
-  (package
-    (name "r-affyio")
-    (version "1.60.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "affyio" version))
-       (sha256
-        (base32
-         "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-zlibbioc" ,r-zlibbioc)))
-    (inputs
-     `(("zlib" ,zlib)))
-    (home-page "https://github.com/bmbolstad/affyio")
-    (synopsis "Tools for parsing Affymetrix data files")
-    (description
-     "This package provides routines for parsing Affymetrix data files based
-upon file format information.  The primary focus is on accessing the CEL and
-CDF file formats.")
-    (license license:lgpl2.0+)))
-
-(define-public r-affy
-  (package
-    (name "r-affy")
-    (version "1.68.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "affy" version))
-       (sha256
-        (base32
-         "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-affyio" ,r-affyio)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-preprocesscore" ,r-preprocesscore)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (inputs
-     `(("zlib" ,zlib)))
-    (home-page "https://bioconductor.org/packages/affy")
-    (synopsis "Methods for affymetrix oligonucleotide arrays")
-    (description
-     "This package contains functions for exploratory oligonucleotide array
-analysis.")
-    (license license:lgpl2.0+)))
-
-(define-public r-vsn
-  (package
-    (name "r-vsn")
-    (version "3.58.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "vsn" version))
-       (sha256
-        (base32
-         "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-biobase" ,r-biobase)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-lattice" ,r-lattice)
-       ("r-limma" ,r-limma)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr))) ; for vignettes
-    (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
-    (synopsis "Variance stabilization and calibration for microarray data")
-    (description
-     "The package implements a method for normalising microarray intensities,
-and works for single- and multiple-color arrays.  It can also be used for data
-from other technologies, as long as they have similar format.  The method uses
-a robust variant of the maximum-likelihood estimator for an
-additive-multiplicative error model and affine calibration.  The model
-incorporates data calibration step (a.k.a.  normalization), a model for the
-dependence of the variance on the mean intensity and a variance stabilizing
-data transformation.  Differences between transformed intensities are
-analogous to \"normalized log-ratios\".  However, in contrast to the latter,
-their variance is independent of the mean, and they are usually more sensitive
-and specific in detecting differential transcription.")
-    (license license:artistic2.0)))
-
-(define-public r-mzid
-  (package
-    (name "r-mzid")
-    (version "1.28.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "mzID" version))
-       (sha256
-        (base32
-         "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2"))))
-    (properties `((upstream-name . "mzID")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-doparallel" ,r-doparallel)
-       ("r-foreach" ,r-foreach)
-       ("r-iterators" ,r-iterators)
-       ("r-plyr" ,r-plyr)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-xml" ,r-xml)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/mzID")
-    (synopsis "Parser for mzIdentML files")
-    (description
-     "This package provides a parser for mzIdentML files implemented using the
-XML package.  The parser tries to be general and able to handle all types of
-mzIdentML files with the drawback of having less pretty output than a vendor
-specific parser.")
-    (license license:gpl2+)))
-
-(define-public r-pcamethods
-  (package
-    (name "r-pcamethods")
-    (version "1.82.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "pcaMethods" version))
-       (sha256
-        (base32
-         "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0"))))
-    (properties `((upstream-name . "pcaMethods")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-mass" ,r-mass)
-       ("r-rcpp" ,r-rcpp)))
-    (home-page "https://github.com/hredestig/pcamethods")
-    (synopsis "Collection of PCA methods")
-    (description
-     "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
-Inverse Non-Linear PCA and the conventional SVD PCA.  A cluster based method
-for missing value estimation is included for comparison.  BPCA, PPCA and
-NipalsPCA may be used to perform PCA on incomplete data as well as for
-accurate missing value estimation.  A set of methods for printing and plotting
-the results is also provided.  All PCA methods make use of the same data
-structure (pcaRes) to provide a common interface to the PCA results.")
-    (license license:gpl3+)))
-
-(define-public r-msnbase
-  (package
-    (name "r-msnbase")
-    (version "2.16.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "MSnbase" version))
-       (sha256
-        (base32
-         "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h"))))
-    (properties `((upstream-name . "MSnbase")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-digest" ,r-digest)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-impute" ,r-impute)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-maldiquant" ,r-maldiquant)
-       ("r-mass" ,r-mass)
-       ("r-mzid" ,r-mzid)
-       ("r-mzr" ,r-mzr)
-       ("r-pcamethods" ,r-pcamethods)
-       ("r-plyr" ,r-plyr)
-       ("r-preprocesscore" ,r-preprocesscore)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rcpp" ,r-rcpp)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-vsn" ,r-vsn)
-       ("r-xml" ,r-xml)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/lgatto/MSnbase")
-    (synopsis "Base functions and classes for MS-based proteomics")
-    (description
-     "This package provides basic plotting, data manipulation and processing
-of mass spectrometry based proteomics data.")
-    (license license:artistic2.0)))
-
-(define-public r-msnid
-  (package
-    (name "r-msnid")
-    (version "1.24.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "MSnID" version))
-       (sha256
-        (base32
-         "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))
-    (properties `((upstream-name . "MSnID")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationhub" ,r-annotationhub)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocstyle" ,r-biocstyle)
-       ("r-biostrings" ,r-biostrings)
-       ("r-data-table" ,r-data-table)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dplyr" ,r-dplyr)
-       ("r-foreach" ,r-foreach)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iterators" ,r-iterators)
-       ("r-msnbase" ,r-msnbase)
-       ("r-msmstests" ,r-msmstests)
-       ("r-mzid" ,r-mzid)
-       ("r-mzr" ,r-mzr)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-purrr" ,r-purrr)
-       ("r-r-cache" ,r-r-cache)
-       ("r-rcpp" ,r-rcpp)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rlang" ,r-rlang)
-       ("r-runit" ,r-runit)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-xtable" ,r-xtable)))
-    (home-page "https://bioconductor.org/packages/MSnID")
-    (synopsis "Utilities for LC-MSn proteomics identifications")
-    (description
-     "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
-from mzIdentML (leveraging the mzID package) or text files.  After collating
-the search results from multiple datasets it assesses their identification
-quality and optimize filtering criteria to achieve the maximum number of
-identifications while not exceeding a specified false discovery rate.  It also
-contains a number of utilities to explore the MS/MS results and assess missed
-and irregular enzymatic cleavages, mass measurement accuracy, etc.")
-    (license license:artistic2.0)))
-
-(define-public r-aroma-light
-  (package
-    (name "r-aroma-light")
-    (version "3.20.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "aroma.light" version))
-       (sha256
-        (base32
-         "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0"))))
-    (properties `((upstream-name . "aroma.light")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-matrixstats" ,r-matrixstats)
-       ("r-r-methodss3" ,r-r-methodss3)
-       ("r-r-oo" ,r-r-oo)
-       ("r-r-utils" ,r-r-utils)))
-    (home-page "https://github.com/HenrikBengtsson/aroma.light")
-    (synopsis "Methods for normalization and visualization of microarray data")
-    (description
-     "This package provides methods for microarray analysis that take basic
-data types such as matrices and lists of vectors.  These methods can be used
-standalone, be utilized in other packages, or be wrapped up in higher-level
-classes.")
-    (license license:gpl2+)))
-
-(define-public r-deseq
-  (package
-    (name "r-deseq")
-    (version "1.39.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "DESeq" version))
-       (sha256
-        (base32
-         "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
-    (properties `((upstream-name . "DESeq")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genefilter" ,r-genefilter)
-       ("r-geneplotter" ,r-geneplotter)
-       ("r-lattice" ,r-lattice)
-       ("r-locfit" ,r-locfit)
-       ("r-mass" ,r-mass)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)))
-    (home-page "https://www-huber.embl.de/users/anders/DESeq/")
-    (synopsis "Differential gene expression analysis")
-    (description
-     "This package provides tools for estimating variance-mean dependence in
-count data from high-throughput genetic sequencing assays and for testing for
-differential expression based on a model using the negative binomial
-distribution.")
-    (license license:gpl3+)))
-
-(define-public r-edaseq
-  (package
-    (name "r-edaseq")
-    (version "2.24.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "EDASeq" version))
-       (sha256
-        (base32
-         "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))
-    (properties `((upstream-name . "EDASeq")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-aroma-light" ,r-aroma-light)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-shortread" ,r-shortread)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/drisso/EDASeq")
-    (synopsis "Exploratory data analysis and normalization for RNA-Seq")
-    (description
-     "This package provides support for numerical and graphical summaries of
-RNA-Seq genomic read data.  Provided within-lane normalization procedures to
-adjust for GC-content effect (or other gene-level effects) on read counts:
-loess robust local regression, global-scaling, and full-quantile
-normalization.  Between-lane normalization procedures to adjust for
-distributional differences between lanes (e.g., sequencing depth):
-global-scaling and full-quantile normalization.")
-    (license license:artistic2.0)))
-
-(define-public r-interactivedisplaybase
-  (package
-    (name "r-interactivedisplaybase")
-    (version "1.28.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "interactiveDisplayBase" version))
-       (sha256
-        (base32
-         "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01"))))
-    (properties
-     `((upstream-name . "interactiveDisplayBase")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-dt" ,r-dt)
-       ("r-shiny" ,r-shiny)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
-    (synopsis "Base package for web displays of Bioconductor objects")
-    (description
-     "This package contains the basic methods needed to generate interactive
-Shiny-based display methods for Bioconductor objects.")
-    (license license:artistic2.0)))
-
-(define-public r-annotationhub
-  (package
-    (name "r-annotationhub")
-    (version "2.22.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "AnnotationHub" version))
-       (sha256
-        (base32
-         "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5"))))
-    (properties `((upstream-name . "AnnotationHub")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biocversion" ,r-biocversion)
-       ("r-curl" ,r-curl)
-       ("r-dplyr" ,r-dplyr)
-       ("r-httr" ,r-httr)
-       ("r-interactivedisplaybase" ,r-interactivedisplaybase)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-yaml" ,r-yaml)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/AnnotationHub")
-    (synopsis "Client to access AnnotationHub resources")
-    (description
-     "This package provides a client for the Bioconductor AnnotationHub web
-resource.  The AnnotationHub web resource provides a central location where
-genomic files (e.g. VCF, bed, wig) and other resources from standard
-locations (e.g. UCSC, Ensembl) can be discovered.  The resource includes
-metadata about each resource, e.g., a textual description, tags, and date of
-modification.  The client creates and manages a local cache of files retrieved
-by the user, helping with quick and reproducible access.")
-    (license license:artistic2.0)))
-
-(define-public r-fastseg
-  (package
-    (name "r-fastseg")
-    (version "1.36.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "fastseg" version))
-       (sha256
-        (base32
-         "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
-    (synopsis "Fast segmentation algorithm for genetic sequencing data")
-    (description
-     "Fastseg implements a very fast and efficient segmentation algorithm.
-It can segment data from DNA microarrays and data from next generation
-sequencing for example to detect copy number segments.  Further it can segment
-data from RNA microarrays like tiling arrays to identify transcripts.  Most
-generally, it can segment data given as a matrix or as a vector.  Various data
-formats can be used as input to fastseg like expression set objects for
-microarrays or GRanges for sequencing data.")
-    (license license:lgpl2.0+)))
-
-(define-public r-keggrest
-  (package
-    (name "r-keggrest")
-    (version "1.30.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "KEGGREST" version))
-       (sha256
-        (base32
-         "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s"))))
-    (properties `((upstream-name . "KEGGREST")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-httr" ,r-httr)
-       ("r-png" ,r-png)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/KEGGREST")
-    (synopsis "Client-side REST access to KEGG")
-    (description
-     "This package provides a package that provides a client interface to the
-@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
-    (license license:artistic2.0)))
-
-(define-public r-gage
-  (package
-    (name "r-gage")
-    (version "2.40.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "gage" version))
-       (sha256
-        (base32
-         "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-go-db" ,r-go-db)
-       ("r-graph" ,r-graph)
-       ("r-keggrest" ,r-keggrest)))
-    (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
-                              "articles/10.1186/1471-2105-10-161"))
-    (synopsis "Generally applicable gene-set enrichment for pathway analysis")
-    (description
-     "GAGE is a published method for gene set (enrichment or GSEA) or pathway
-analysis.  GAGE is generally applicable independent of microarray or RNA-Seq
-data attributes including sample sizes, experimental designs, assay platforms,
-and other types of heterogeneity.  The gage package provides functions for
-basic GAGE analysis, result processing and presentation.  In addition, it
-provides demo microarray data and commonly used gene set data based on KEGG
-pathways and GO terms.  These functions and data are also useful for gene set
-analysis using other methods.")
-    (license license:gpl2+)))
-
-(define-public r-genomicfiles
-  (package
-    (name "r-genomicfiles")
-    (version "1.26.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "GenomicFiles" version))
-       (sha256
-        (base32
-         "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz"))))
-    (properties `((upstream-name . "GenomicFiles")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixgenerics" ,r-matrixgenerics)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
-    (home-page "https://bioconductor.org/packages/GenomicFiles")
-    (synopsis "Distributed computing by file or by range")
-    (description
-     "This package provides infrastructure for parallel computations
-distributed by file or by range.  User defined mapper and reducer functions
-provide added flexibility for data combination and manipulation.")
-    (license license:artistic2.0)))
-
-(define-public r-complexheatmap
-  (package
-    (name "r-complexheatmap")
-    (version "2.6.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ComplexHeatmap" version))
-       (sha256
-        (base32
-         "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x"))))
-    (properties
-     `((upstream-name . "ComplexHeatmap")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-cairo" ,r-cairo)
-       ("r-circlize" ,r-circlize)
-       ("r-clue" ,r-clue)
-       ("r-colorspace" ,r-colorspace)
-       ("r-digest" ,r-digest)
-       ("r-getoptlong" ,r-getoptlong)
-       ("r-globaloptions" ,r-globaloptions)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-png" ,r-png)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page
-     "https://github.com/jokergoo/ComplexHeatmap")
-    (synopsis "Making Complex Heatmaps")
-    (description
-     "Complex heatmaps are efficient to visualize associations between
-different sources of data sets and reveal potential structures.  This package
-provides a highly flexible way to arrange multiple heatmaps and supports
-self-defined annotation graphics.")
-    (license license:gpl2+)))
-
-(define-public r-dirichletmultinomial
-  (package
-    (name "r-dirichletmultinomial")
-    (version "1.32.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "DirichletMultinomial" version))
-       (sha256
-        (base32
-         "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk"))))
-    (properties
-     `((upstream-name . "DirichletMultinomial")))
-    (build-system r-build-system)
-    (inputs
-     `(("gsl" ,gsl)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://bioconductor.org/packages/DirichletMultinomial")
-    (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
-    (description
-     "Dirichlet-multinomial mixture models can be used to describe variability
-in microbial metagenomic data.  This package is an interface to code
-originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
-1-15.")
-    (license license:lgpl3)))
-
-(define-public r-ensembldb
-  (package
-    (name "r-ensembldb")
-    (version "2.14.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ensembldb" version))
-       (sha256
-        (base32
-         "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationfilter" ,r-annotationfilter)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-curl" ,r-curl)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/jotsetung/ensembldb")
-    (synopsis "Utilities to create and use Ensembl-based annotation databases")
-    (description
-     "The package provides functions to create and use transcript-centric
-annotation databases/packages.  The annotation for the databases are directly
-fetched from Ensembl using their Perl API.  The functionality and data is
-similar to that of the TxDb packages from the @code{GenomicFeatures} package,
-but, in addition to retrieve all gene/transcript models and annotations from
-the database, the @code{ensembldb} package also provides a filter framework
-allowing to retrieve annotations for specific entries like genes encoded on a
-chromosome region or transcript models of lincRNA genes.")
-    ;; No version specified
-    (license license:lgpl3+)))
-
-(define-public r-organismdbi
-  (package
-    (name "r-organismdbi")
-    (version "1.32.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "OrganismDbi" version))
-       (sha256
-        (base32
-         "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw"))))
-    (properties `((upstream-name . "OrganismDbi")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-dbi" ,r-dbi)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-graph" ,r-graph)
-       ("r-iranges" ,r-iranges)
-       ("r-rbgl" ,r-rbgl)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://bioconductor.org/packages/OrganismDbi")
-    (synopsis "Software to enable the smooth interfacing of database packages")
-    (description "The package enables a simple unified interface to several
-annotation packages each of which has its own schema by taking advantage of
-the fact that each of these packages implements a select methods.")
-    (license license:artistic2.0)))
-
-(define-public r-biovizbase
-  (package
-    (name "r-biovizbase")
-    (version "1.38.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "biovizBase" version))
-       (sha256
-        (base32
-         "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq"))))
-    (properties `((upstream-name . "biovizBase")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationfilter" ,r-annotationfilter)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dichromat" ,r-dichromat)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-hmisc" ,r-hmisc)
-       ("r-iranges" ,r-iranges)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rlang" ,r-rlang)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
-    (home-page "https://bioconductor.org/packages/biovizBase")
-    (synopsis "Basic graphic utilities for visualization of genomic data")
-    (description
-     "The biovizBase package is designed to provide a set of utilities, color
-schemes and conventions for genomic data.  It serves as the base for various
-high-level packages for biological data visualization.  This saves development
-effort and encourages consistency.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
@@ -10549,13 +9089,13 @@ browser.")
         (revision "1"))
     (package
       (name "f-seq")
-      (version (string-append "1.1-" revision "." (string-take commit 7)))
+      (version (git-version "1.1" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
                       (url "https://github.com/aboyle/F-seq")
                       (commit commit)))
-                (file-name (string-append name "-" version))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
                   "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))
@@ -10613,7 +9153,7 @@ Browser.")
        (uri (git-reference
              (url "https://github.com/FelixKrueger/Bismark")
              (commit version)))
-       (file-name (string-append name "-" version "-checkout"))
+       (file-name (git-file-name name version))
        (sha256
         (base32
          "0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9"))))
@@ -11753,7 +10293,7 @@ once.  This package provides tools to perform Drop-seq analyses.")
 (define-public pigx-rnaseq
   (package
     (name "pigx-rnaseq")
-    (version "0.0.10")
+    (version "0.0.13")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
@@ -11761,7 +10301,7 @@ once.  This package provides tools to perform Drop-seq analyses.")
                                   "/pigx_rnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "0z3hr120wk2vrlmlpz1vp3n9wy3rq4y2mnzh2vf08qgqn2xfdwcw"))))
+                "0z9zid2c8q16lfzlnjd63nparknhv31qgv4h79algmvhkakm2pgk"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-tests? #f             ; not supported
@@ -11771,19 +10311,17 @@ once.  This package provides tools to perform Drop-seq analyses.")
          (add-after 'unpack 'disable-resource-intensive-test
            (lambda _
              (substitute* "Makefile.in"
-               (("(^  tests/test_trim_galore/test.sh).*" _ m) m)
                (("^  tests/test_multiqc/test.sh") "")
-               (("^  test.sh") ""))
-             #t)))))
+               (("^  test.sh") "")))))))
     (inputs
      `(("coreutils" ,coreutils)
        ("sed" ,sed)
        ("gzip" ,gzip)
        ("snakemake" ,snakemake)
-       ("fastqc" ,fastqc)
        ("multiqc" ,multiqc)
        ("star" ,star-for-pigx)
-       ("trim-galore" ,trim-galore)
+       ("hisat2" ,hisat2)
+       ("fastp" ,fastp)
        ("htseq" ,htseq)
        ("samtools" ,samtools)
        ("r-minimal" ,r-minimal)
@@ -12032,6 +10570,54 @@ and interactive quality reports.  The pipeline is designed to work with UMI
 based methods.")
     (license license:gpl3+)))
 
+(define-public pigx-sars-cov2-ww
+  (package
+    (name "pigx-sars-cov2-ww")
+    (version "0.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/"
+                                  "releases/download/v" version
+                                  "/pigx_sars-cov2-ww-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1h1rfl3dyf7pid74xxgiyr4x1l5yj000wcz5crm1bdbaz8p7b7ic"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("bash-minimal" ,bash-minimal)
+       ("bwa" ,bwa)
+       ("ensembl-vep" ,ensembl-vep)
+       ("fastqc" ,fastqc)
+       ("kraken2" ,kraken2)
+       ("krona-tools" ,krona-tools)
+       ("lofreq" ,lofreq)
+       ("multiqc" ,multiqc)
+       ("prinseq" ,prinseq)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-wrapper" ,python-wrapper)
+       ("r-base64url" ,r-base64url)
+       ("r-dplyr" ,r-dplyr)
+       ("r-dt" ,r-dt)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-magrittr" ,r-magrittr)
+       ("r-minimal" ,r-minimal)
+       ("r-plotly" ,r-plotly)
+       ("r-qpcr" ,r-qpcr)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-stringr" ,r-stringr)
+       ("r-tidyr" ,r-tidyr)
+       ("samtools" ,samtools)
+       ("snakemake" ,snakemake)))
+    (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
+    (synopsis "Analysis pipeline for wastewater sequencing")
+    (description "PiGx SARS-CoV-2 is a pipeline for analysing data from
+sequenced wastewater samples and identifying given variants-of-concern of
+SARS-CoV-2.  The pipeline can be used for continuous sampling.  The output
+report will provide an intuitive visual overview about the development of
+variant abundance over time and location.")
+    (license license:gpl3+)))
+
 (define-public pigx
   (package
     (name "pigx")
@@ -12190,7 +10776,7 @@ version does count multisplits.")
 (define-public minimap2
   (package
     (name "minimap2")
-    (version "2.17")
+    (version "2.18")
     (source
      (origin
        (method url-fetch)
@@ -12199,11 +10785,13 @@ version does count multisplits.")
                            "minimap2-" version ".tar.bz2"))
        (sha256
         (base32
-         "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn"))
-       (patches (search-patches "minimap2-aarch64-support.patch"))))
+         "1d7fvdqcqd6wns875rkyd7f34ii15gc9l1sivd2wbbpcb0fi0mbs"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there are none
+       #:modules ((guix build utils)
+                  (guix build gnu-build-system)
+                  (srfi srfi-26))
        #:make-flags
        (list (string-append "CC=" ,(cc-for-target))
              (let ((system ,(or (%current-target-system)
@@ -12226,10 +10814,30 @@ version does count multisplits.")
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
+                    (lib (string-append out "/lib"))
+                    (inc (string-append out "/include"))
                     (man (string-append out "/share/man/man1")))
                (install-file "minimap2" bin)
-               (mkdir-p man)
-               (install-file "minimap2.1" man))
+               (install-file "libminimap2.a" lib)
+               (install-file "minimap2.1" man)
+               (map (cut install-file <> inc)
+                    (find-files "." "\\.h$"))
+               ;; Not this file.
+               (delete-file (string-append inc "/emmintrin.h"))
+               (mkdir-p (string-append lib "/pkgconfig"))
+               (with-output-to-file (string-append lib "/pkgconfig/minimap2.pc")
+                (lambda _
+                  (format #t "prefix=~a~@
+                          exec_prefix=${prefix}~@
+                          libdir=${exec_prefix}/lib~@
+                          includedir=${prefix}/include~@
+                          ~@
+                          Name: libminimap2~@
+                          Version: ~a~@
+                          Description: A versatile pairwise aligner for genomic and spliced nucleotide sequence~@
+                          Libs: -L${libdir} -lminimap2~@
+                          Cflags: -I${includedir}~%"
+                          out ,version))))
              #t)))))
     (inputs
      `(("zlib" ,zlib)))
@@ -12346,6 +10954,96 @@ contigs alone.")
     (license (list license:gpl2+        ; bundled ogdf
                    license:gpl3+))))
 
+(define-public libmaus2
+  (package
+    (name "libmaus2")
+    (version "2.0.786")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://gitlab.com/german.tischler/libmaus2")
+                    (commit (string-append version "-release-20210531143054"))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1rxakmwjcx2yq5sjh3v849f7dfw4xzc2fyzf6s28s3p95z84w564"))))
+    (build-system gnu-build-system)
+    ;; The test suite attempts to execute ../test-driver, which does not exist.
+    (arguments '(#:tests? #false))
+    (propagated-inputs
+     `(("zlib" ,zlib)))
+    (native-inputs
+     `(("gcc" ,gcc-10)                   ;Code has C++17 requirements
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://gitlab.com/german.tischler/libmaus2")
+    (synopsis "Collection of data structures and algorithms useful for bioinformatics")
+    (description "libmaus2 is a collection of data structures and
+algorithms.  It contains:
+
+@itemize
+@item I/O classes (single byte and UTF-8);
+@item @code{bitio} classes (input, output and various forms of bit level
+  manipulation);
+@item text indexing classes (suffix and LCP array, fulltext and minute (FM),
+  etc.);
+@item BAM sequence alignment files input/output (simple and collating);
+and many lower level support classes.
+@end itemize\n")
+    ;; The code is explicitly available under the terms of either GPLv2 or
+    ;; GPLv3 according to the AUTHORS file, though most files have a GPLv3+
+    ;; license header.
+    (license (list license:gpl2+ license:gpl3+))))
+
+(define-public biobambam2
+  (package
+    (name "biobambam2")
+    (version "2.0.182")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://gitlab.com/german.tischler/biobambam2")
+                    (commit (string-append version "-release-20210412001032"))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0b7w7a2a7hpkgrdn0n7hy4pilzrj82zqrh7q4bg1l0cd6bqr60m5"))))
+    (build-system gnu-build-system)
+    (arguments
+     ;; The test suite attempts to execute ../test-driver, which does not exist.
+     `(#:tests? #false
+       #:configure-flags
+       (list (string-append "--with-libmaus2="
+                            (assoc-ref %build-inputs "libmaus2")))))
+    (inputs
+     `(("libmaus2" ,libmaus2)
+       ("xerces-c" ,xerces-c)))
+    (native-inputs
+     `(("gcc" ,gcc-10)                  ;Code has C++17 requirements
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://gitlab.com/german.tischler/biobambam2")
+    (synopsis "Tools for processing BAM files")
+    (description "This package contains some tools for processing BAM files
+including:
+
+@itemize
+@item bamsormadup: parallel sorting and duplicate marking
+@item bamcollate2: reads BAM and writes BAM reordered such that alignment or
+  collated by query name
+@item bammarkduplicates: reads BAM and writes BAM with duplicate alignments
+  marked using the BAM flags field
+@item bammaskflags: reads BAM and writes BAM while masking (removing) bits
+  from the flags column
+@item bamrecompress: reads BAM and writes BAM with a defined compression
+  setting.  This tool is capable of multi-threading.
+@item bamsort: reads BAM and writes BAM resorted by coordinates or query name
+@item bamtofastq: reads BAM and writes FastQ; output can be collated or
+  uncollated by query name.
+@end itemize
+")
+    ;; The COPYING file states that the code is distributed under version 3 of
+    ;; the GPL, but the license headers include the "or later" clause.
+    (license license:gpl3+)))
+
 (define-public r-circus
   (package
     (name "r-circus")
@@ -12501,17 +11199,80 @@ spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA)
 in RNA-seq data.")
       (license license:gpl3))))
 
+(define-public fit-sne
+  (package
+    (name "fit-sne")
+    (version "1.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/KlugerLab/FIt-SNE")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1imq4577awc226wvygf94kpz156qdfw8xl0w0f7ss4w10lhmpmf5"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #false ; there are none
+       #:phases
+       ;; There is no build system.
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'build
+           (lambda _
+             (invoke "g++" "-std=c++11" "-O3"
+                     "src/sptree.cpp"
+                     "src/tsne.cpp"
+                     "src/nbodyfft.cpp"
+                     "-o" "bin/fast_tsne"
+                     "-pthread" "-lfftw3" "-lm"
+                     "-Wno-address-of-packed-member")))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (share (string-append out "/share/fit-sne")))
+               (for-each (lambda (file) (install-file file bin))
+                         (find-files "bin"))
+
+               (substitute* "fast_tsne.R"
+                 (("^FAST_TSNE_SCRIPT_DIR.*")
+                  (string-append "FAST_TSNE_SCRIPT_DIR = \"" out "\"\n")))
+               (install-file "fast_tsne.R" share)))))))
+    (inputs
+     `(("fftw" ,fftw)))
+    (home-page "https://github.com/KlugerLab/FIt-SNE")
+    (synopsis "Fast Fourier Transform-accelerated interpolation-based t-SNE")
+    (description "@dfn{t-Stochastic Neighborhood Embedding} (t-SNE) is a
+method for dimensionality reduction and visualization of high dimensional
+datasets.  A popular implementation of t-SNE uses the Barnes-Hut algorithm to
+approximate the gradient at each iteration of gradient descent.  This
+implementation differs in these ways:
+
+@itemize
+@item Instead of approximating the N-body simulation using Barnes-Hut, we
+  interpolate onto an equispaced grid and use FFT to perform the convolution.
+@item Instead of computing nearest neighbors using vantage-point trees, we
+  approximate nearest neighbors using the Annoy library.  The neighbor lookups
+  are multithreaded to take advantage of machines with multiple cores.
+@end itemize
+")
+    ;; See LICENSE.txt for details on what license applies to what files.
+    (license (list license:bsd-4 license:expat license:asl2.0))))
+
 (define-public python-scanpy
   (package
     (name "python-scanpy")
-    (version "1.4.6")
+    (version "1.7.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "scanpy" version))
        (sha256
         (base32
-         "0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l"))))
+         "0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -12522,12 +11283,28 @@ in RNA-seq data.")
              (delete-file-recursively "scanpy/tests/notebooks")
              (delete-file "scanpy/tests/test_clustering.py")
              (delete-file "scanpy/tests/test_datasets.py")
+             (delete-file "scanpy/tests/test_highly_variable_genes.py")
 
              ;; TODO: I can't get the plotting tests to work, even with Xvfb.
              (delete-file "scanpy/tests/test_plotting.py")
              (delete-file "scanpy/tests/test_preprocessing.py")
              (delete-file "scanpy/tests/test_read_10x.py")
 
+             ;; The following tests need anndata.tests, which aren't included
+             ;; in the final python-anndata package.
+             (delete-file "scanpy/tests/test_combat.py")
+             (delete-file "scanpy/tests/test_embedding_plots.py")
+             (delete-file "scanpy/tests/test_normalization.py")
+             (delete-file "scanpy/tests/test_pca.py")
+             (delete-file "scanpy/tests/external/test_scrublet.py")
+
+             ;; The following tests requires 'scanorama', which isn't
+             ;; packaged yet.
+             (delete-file "scanpy/tests/external/test_scanorama_integrate.py")
+
+             (setenv "PYTHONPATH"
+                     (string-append (getcwd) ":"
+                                    (getenv "PYTHONPATH")))
              (invoke "pytest"))))))
     (propagated-inputs
      `(("python-anndata" ,python-anndata)
@@ -12548,11 +11325,14 @@ in RNA-seq data.")
        ("python-seaborn" ,python-seaborn)
        ("python-statsmodels" ,python-statsmodels)
        ("python-tables" ,python-tables)
+       ("python-pytoml" ,python-pytoml)
        ("python-tqdm" ,python-tqdm)
        ("python-umap-learn" ,python-umap-learn)))
     (native-inputs
-     `(("python-pytest" ,python-pytest)
-       ("python-setuptools-scm" ,python-setuptools-scm)))
+     `(("python-leidenalg" ,python-leidenalg)
+       ("python-pytest" ,python-pytest)
+       ("python-setuptools-scm" ,python-setuptools-scm)
+       ("python-sinfo" ,python-sinfo)))
     (home-page "https://github.com/theislab/scanpy")
     (synopsis "Single-Cell Analysis in Python.")
     (description "Scanpy is a scalable toolkit for analyzing single-cell gene
@@ -12874,15 +11654,39 @@ fasta subsequences.")
 (define-public python-cooler
   (package
     (name "python-cooler")
-    (version "0.8.7")
+    (version "0.8.11")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cooler" version))
        (sha256
         (base32
-         "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp"))))
+         "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-tests
+           (lambda _
+             (substitute* "tests/test_create.py"
+              (("def test_roundtrip")
+                 (string-append "@pytest.mark.skip(reason=\"requires network "
+                                "access to genome.ucsc.edu\")\n"
+                                "def test_roundtrip")))
+             (substitute* "tests/test_util.py"
+              (("def test_fetch_chromsizes")
+                 (string-append "@pytest.mark.skip(reason=\"requires network "
+                                "access to genome.ucsc.edu\")\n"
+                                "def test_fetch_chromsizes")))
+             ;; This test depends on ipytree, which contains a lot of minified
+             ;; JavaScript.
+             (substitute* "tests/test_fileops.py"
+               (("def test_print_trees")
+                "def _test_print_trees"))))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "python" "-m" "pytest" "-v")))))))
     (propagated-inputs
      `(("python-asciitree" ,python-asciitree)
        ("python-biopython" ,python-biopython)
@@ -12898,11 +11702,17 @@ fasta subsequences.")
        ("python-pysam" ,python-pysam)
        ("python-pyyaml" ,python-pyyaml)
        ("python-scipy" ,python-scipy)
-       ("python-simplejson" ,python-simplejson)))
+       ("python-simplejson" ,python-simplejson)
+       ("python-six" ,python-six)
+       ("python-sparse" ,python-sparse)))
     (native-inputs
-     `(("python-mock" ,python-mock)
-       ("python-pytest" ,python-pytest)))
-    (home-page "https://github.com/mirnylab/cooler")
+     `(("python-codecov" ,python-codecov)
+       ("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-flake8" ,python-pytest-flake8)))
+    ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
+    (home-page "https://github.com/open2c/cooler")
     (synopsis "Sparse binary format for genomic interaction matrices")
     (description
      "Cooler is a support library for a sparse, compressed, binary persistent
@@ -14701,7 +13511,7 @@ manipulations on VCF files.")
 (define-public freebayes
   (package
     (name "freebayes")
-    (version "1.3.3")
+    (version "1.3.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -14709,8 +13519,7 @@ manipulations on VCF files.")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8"))
-              (patches (search-patches "freebayes-devendor-deps.patch"))
+               (base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -14722,8 +13531,7 @@ manipulations on VCF files.")
        ("htslib" ,htslib)
        ("smithwaterman" ,smithwaterman)
        ("tabixpp" ,tabixpp)
-       ("vcflib" ,vcflib)
-       ("zlib" ,zlib)))
+       ("vcflib" ,vcflib)))
     (native-inputs
      `(("bash-tap" ,bash-tap)
        ("bc" ,bc)
@@ -14756,13 +13564,13 @@ manipulations on VCF files.")
                   (string-append bash-tap "/bin/bash-tap-bootstrap"))
                  (("source.*bash-tap-bootstrap")
                   (string-append "source " bash-tap "/bin/bash-tap-bootstrap")))
-               (substitute* "meson.build"
-                  ;; Some inputs aren't actually needed.
-                 ((".*bamtools/src.*") "")
-                 ((".*multichoose.*") ""))
                (substitute* '("src/BedReader.cpp"
                               "src/BedReader.h")
                  (("../intervaltree/IntervalTree.h") "IntervalTree.h"))
+               (substitute* "meson.build"
+                 ;; Our pkg-config file is vcflib.pc
+                 (("libvcflib") "vcflib")
+                 (("vcflib_inc,") ""))
                #t)))
          (add-after 'unpack 'unpack-submodule-sources
            (lambda* (#:key inputs #:allow-other-keys)
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 4e82da869e..739870dc77 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -431,6 +431,7 @@ a multi-paradigm automated test framework for C++ and Objective-C.")
               (uri (git-reference
                     (url "git://git.liw.fi/cmdtest/")
                     (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
                 "1yhcwsqcpckkq5kw3h07k0xg6infyiyzq9ni3nqphrzxis7hxjf1"))))
@@ -697,8 +698,8 @@ generation.")
     (license license:bsd-3)))
 
 (define-public googletest-1.8
-  (package/inherit
-   googletest
+  (package
+    (inherit googletest)
    (version "1.8.1")
    (source (origin
              (method git-fetch)
@@ -1144,8 +1145,8 @@ contacting the real http server.")
 ;; python-bleach 3.1.0 requires this ancient version of pytest-runner.
 ;; Remove once no longer needed.
 (define-public python-pytest-runner-2
-  (package/inherit
-   python-pytest-runner
+  (package
+    (inherit python-pytest-runner)
    (version "2.12.2")
    (source (origin
              (method url-fetch)
diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm
index f06767f305..6a98867cc8 100644
--- a/gnu/packages/chromium.scm
+++ b/gnu/packages/chromium.scm
@@ -163,6 +163,7 @@
     "third_party/google_input_tools/third_party/closure_library/third_party/closure" ;Expat
     "third_party/googletest" ;BSD-3
     "third_party/harfbuzz-ng" ;Expat
+    "third_party/highway" ;ASL2.0
     "third_party/hunspell" ;MPL1.1/GPL2+/LGPL2.1+
     "third_party/iccjpeg" ;IJG
     "third_party/inspector_protocol" ;BSD-3
@@ -179,6 +180,7 @@
     "third_party/libaom/source/libaom/third_party/fastfeat" ;BSD-3
     "third_party/libaom/source/libaom/third_party/vector" ;Expat
     "third_party/libaom/source/libaom/third_party/x86inc" ;ISC
+    "third_party/libjxl" ;ASL2.0
     "third_party/libgav1" ;ASL2.0
     "third_party/libgifcodec" ;MPL1.1/GPL2+/LGPL2.1+, BSD-3, BSD-2
     "third_party/libjingle_xmpp" ;BSD-3
@@ -239,7 +241,6 @@
     "third_party/rnnoise" ;BSD-3
     "third_party/ruy" ;ASL2.0
     "third_party/s2cellid" ;ASL2.0
-    "third_party/schema_org" ;CC-BY-SA3.0
     "third_party/securemessage" ;ASL2.0
     "third_party/shell-encryption" ;ASL2.0
     "third_party/skia" ;BSD-3
@@ -274,6 +275,7 @@
     "third_party/wayland-protocols" ;Expat
     "third_party/web-animations-js" ;ASL2.0
     "third_party/webdriver" ;ASL2.0
+    "third_party/webgpu-cts" ;BSD-3
     "third_party/webrtc" ;BSD-3
     "third_party/webrtc/common_audio/third_party/ooura" ;Non-copyleft
     "third_party/webrtc/common_audio/third_party/spl_sqrt_floor" ;Public domain
@@ -320,14 +322,14 @@
                   (string-append "ungoogled-chromium-" category "-" name))))
     (sha256 (base32 hash))))
 
-(define %chromium-version "90.0.4430.212")
+(define %chromium-version "91.0.4472.77")
 (define %debian-revision "debian/90.0.4430.85-1")
-(define %ungoogled-revision "90.0.4430.85-1-11-g3184907")
+;; Note: use 'git describe --long' even for exact tags to placate the
+;; custom version format for ungoogled-chromium.
+(define %ungoogled-revision "91.0.4472.77-1-0-g6802c88")
 
 (define %debian-patches
-  (list (debian-patch "fixes/missing-includes.patch"
-                      "1f0drxp1cy76g71rkkzxxbwixn03yn9b0q22vb0mb6h2qk6cw92q")
-        (debian-patch "fixes/nomerge.patch"
+  (list (debian-patch "fixes/nomerge.patch"
                       "0lybs2b5gk08j8cr6vjrs9d3drd7qfw013z2r0y00by8dnpm74i3")
         (debian-patch "system/nspr.patch"
                       "1gdirn1k1i841l8zp8xgr95kl16b5nx827am9rcxj8sfkm8hgkn3")
@@ -344,7 +346,7 @@
     (file-name (git-file-name "ungoogled-chromium" %ungoogled-revision))
     (sha256
      (base32
-      "18xfwgkw3xarxcgnzvyv70h4icyqh3k8lfx6fvhp7fsr6x20sai0"))))
+      "1jfmmkw1y4rcjfgsm7b4v2lrgd3sks5qpajvq0djflbhkpsqxfk0"))))
 
 (define %guix-patches
   (list (local-file
@@ -399,6 +401,11 @@
 
           (format #t "Replacing GN files...~%")
           (force-output)
+          ;; XXX: Chromium no longer relies on overriding ICU's UCHAR_TYPE,
+          ;; but the unbundling code was not updated.  Remove for M92.
+          (substitute* "build/linux/unbundle/icu.gn"
+            (("\"UCHAR_TYPE=uint16_t\",")
+             ""))
           (substitute* "tools/generate_shim_headers/generate_shim_headers.py"
             ;; The "is_official_build" configure option enables certain
             ;; release optimizations like those used in the commercial
@@ -481,7 +488,7 @@
                                   %chromium-version ".tar.xz"))
               (sha256
                (base32
-                "17nmhrkl81qqvzbh861k2mmifncx4wg1mv1fmn52f8gzn461vqdb"))
+                "0c8vj3gq3nmb7ssiwj6875g0a8hcprss1a4gqw9h7llqywza9ma5"))
               (modules '((guix build utils)))
               (snippet (force ungoogled-chromium-snippet))))
     (build-system gnu-build-system)
@@ -630,6 +637,12 @@
                (("include \"third_party/lcms/include/lcms2\\.h\"")
                 "include \"lcms2.h\""))
 
+             ;; Add missing include statement.
+             (substitute* "third_party/pdfium/core/fxcodec/png/png_decoder.cpp"
+               (("#include \"core/fxcodec/fx_codec.h\"" all)
+                (string-append all
+                               "\n#include \"core/fxcodec/fx_codec_def.h\"")))
+
              (substitute*
                  "third_party/breakpad/breakpad/src/common/linux/libcurl_wrapper.h"
                (("include \"third_party/curl")
@@ -852,7 +865,7 @@
        ("glib" ,glib)
        ("gtk+" ,gtk+)
        ("harfbuzz" ,harfbuzz)
-       ("icu4c" ,icu4c-68)
+       ("icu4c" ,icu4c-69)
        ("lcms" ,lcms)
        ("libevent" ,libevent)
        ("libffi" ,libffi)
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index 62f197c2f9..e3918fb724 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -73,8 +73,8 @@
                 (file-name (string-append name "-" version "-checkout")))))))
 
 (define-public cuirass
-  (let ((commit "31fd4d4fe107d86f5e202510e177726a1f49e828")
-        (revision "17"))
+  (let ((commit "21202760c0d15c99b69ef235ff129ab9cb478186")
+        (revision "25"))
     (package
       (name "cuirass")
       (version (git-version "1.0.0" revision commit))
@@ -87,7 +87,7 @@
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "08phqr0sfi6hkzrqhqsh9ri9434sd41qg1b5vijbadgsj1ql33rw"))))
+           "1bzzycz7jmmrph730p8d3q2h76ab6i8j72wblm3w0szf8vimcqfk"))))
       (build-system gnu-build-system)
       (arguments
        `(#:modules ((guix build utils)
@@ -141,7 +141,7 @@
                       (guix   (assoc-ref inputs "guix"))
                       (deps   (list avahi gcrypt json zmq squee git bytes
                                     fibers zlib matd tls mail guix))
-                      (guile  (assoc-ref %build-inputs "guile"))
+                      (guile  (assoc-ref inputs "guile"))
                       (effective
                        (read-line
                         (open-pipe* OPEN_READ
diff --git a/gnu/packages/cluster.scm b/gnu/packages/cluster.scm
index 01996591c7..e643cc58f9 100644
--- a/gnu/packages/cluster.scm
+++ b/gnu/packages/cluster.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Andrew Miloradovsky <andrew@interpretmath.pw>
 ;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2021 Dion Mendel <guix@dm9.info>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -33,6 +34,7 @@
   #:use-module (gnu packages linux)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages sqlite)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls))
 
@@ -186,7 +188,7 @@ independently or together to provide resilient infrastructures.")
 (define-public libraft
   (package
     (name "libraft")
-    (version "0.9.11")
+    (version "0.10.1")
     (home-page "https://github.com/canonical/raft")
     (source (origin
               (method git-fetch)
@@ -195,7 +197,7 @@ independently or together to provide resilient infrastructures.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "00rsq4z9nykmf7r5rlpv1y6bvckcmg3zv57vh1h681y5pij6cch1"))))
+                "18idj53vnl5fx1ja1zlp8kiwmdxgwjxsi88rdql0pbh0484b92a3"))))
     (arguments '(#:configure-flags '("--enable-uv")
                  #:phases
                  (modify-phases %standard-phases
@@ -220,3 +222,42 @@ that, a pluggable interface defines the I/O implementation for networking
 (send/receive RPC messages) and disk persistence (store log entries and
 snapshots).")
     (license license:asl2.0)))
+
+(define-public libdqlite
+  (package
+    (name "libdqlite")
+    (version "1.7.0")
+    (home-page "https://github.com/canonical/dqlite")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference (url home-page)
+                                  (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "15cg8yl3n7lcg0qyg0byciz8v6y200ghmzzkwpdzggy3m6c168wl"))))
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-failing-tests
+           (lambda _
+             (substitute* "Makefile.am"
+               ;; Test client/query sometimes fails.
+               ;; The actual tested asserts succeed, but there appears to be a
+               ;; race condition when tearing down the test server.
+               ((".*test_client.c.*") "")))))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libraft" ,libraft)
+       ("libuv" ,libuv)))
+    (propagated-inputs
+     `(("sqlite" ,sqlite)))  ; dqlite.h includes sqlite3.h
+    (build-system gnu-build-system)
+    (synopsis "Distributed SQLite")
+    (description "dqlite is a C library that implements an embeddable and replicated
+SQL database engine with high-availability and automatic failover.")
+    (license license:lgpl3)))
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 64816a30c0..cc91bcfaa4 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -864,7 +864,15 @@ time for compression ratio.")
                                   "squashfs" version ".tar.gz"))
               (sha256
                (base32
-                "0zmhvczscqz0mzh4b9m8m42asq14db0a6lc8clp5ljq5ybrv70d9"))))
+                "0zmhvczscqz0mzh4b9m8m42asq14db0a6lc8clp5ljq5ybrv70d9"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Fix build with -fno-common (default in GCC 10).
+                  ;; Remove for squashfs-tools > 4.4.
+                  (substitute* "squashfs-tools/mksquashfs.h"
+                    (("struct cache \\*bwriter_buffer" all)
+                     (string-append "extern " all)))))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no check target
@@ -1008,7 +1016,7 @@ tarballs.")
 (define-public libjcat
   (package
     (name "libjcat")
-    (version "0.1.7")
+    (version "0.1.8")
     (source
      (origin
        (method git-fetch)
@@ -1018,7 +1026,7 @@ tarballs.")
          (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "110c8h3p7m4ibrfvgja592z7j5h88qqanllxsvmxkjz3b129i02r"))))
+        (base32 "18qkyg19r7fxzv93kar5n808n3582ygjmqwa7rnyg5y4b6hnwihl"))))
     (build-system meson-build-system)
     (native-inputs
      `(("gobject-introspection" ,gobject-introspection)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8709cd21fa..2e7e9041c6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -33,7 +33,6 @@
 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
-;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -351,6 +350,54 @@ easier.")
 for authoring journal articles and conference submissions.")
     (license license:gpl3)))
 
+(define-public r-benchmarkmedata
+  (package
+    (name "r-benchmarkmedata")
+    (version "1.0.4")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "benchmarkmeData" version))
+              (sha256
+               (base32
+                "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-tibble" ,r-tibble)))
+    (home-page "https://github.com/csgillespie/benchmarkme-data")
+    (synopsis "Data set for the @code{benchmarkme} package")
+    (description "This package contains the data set for the crowd-sourced
+benchmarks from running the @code{benchmarkme} package.")
+    (license license:gpl2+)))
+
+(define-public r-benchmarkme
+  (package
+    (name "r-benchmarkme")
+    (version "1.0.7")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "benchmarkme" version))
+              (sha256
+               (base32
+                "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (propagated-inputs
+     `(("r-benchmarkmedata" ,r-benchmarkmedata)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dplyr" ,r-dplyr)
+       ("r-foreach" ,r-foreach)
+       ("r-httr" ,r-httr)
+       ("r-matrix" ,r-matrix)
+       ("r-tibble" ,r-tibble)))
+    (home-page "https://csgillespie.github.io/benchmarkme/")
+    (synopsis "Crowd-sourced system benchmarks")
+    (description "This package provides functionality to benchmark your CPU
+and compare against other CPUs.  Also provides functions for obtaining system
+specifications, such as RAM, CPU type, and R version.")
+    (license license:gpl2+)))
+
 (define-public r-bezier
   (package
     (name "r-bezier")
@@ -671,6 +718,28 @@ provides methods for automatically determining breaks and labels for axes and
 legends.")
     (license license:expat)))
 
+(define-public r-pacman
+  (package
+    (name "r-pacman")
+    (version "0.5.1")
+    (source (origin
+             (method url-fetch)
+             (uri (cran-uri "pacman" version))
+             (sha256
+              (base32
+               "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-remotes" ,r-remotes)))
+    (home-page "https://github.com/trinker/pacman")
+    (synopsis "Package Management Tool")
+    (description "This package provides tools to more conveniently perform
+tasks associated with add-on packages.  @code{pacman} conveniently wraps
+library and package related functions and names them in an intuitive and
+consistent fashion.  It seeks to combine functionality from lower level
+functions which can speed up workflow.")
+    (license license:gpl2)))
+
 (define-public r-pheatmap
   (package
     (name "r-pheatmap")
@@ -1130,6 +1199,29 @@ without affecting the current R process at all.  This package does exactly
 that.")
     (license license:expat)))
 
+(define-public r-depmixs4
+  (package
+    (name "r-depmixs4")
+    (version "1.5-0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "depmixS4" version))
+              (sha256
+               (base32
+                "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8"))))
+    (propagated-inputs
+     `(("r-nnet" ,r-nnet)
+       ("r-nlme" ,r-nlme)
+       ("r-mass" ,r-mass)
+       ("r-rsolnp" ,r-rsolnp)))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/depmixS4/")
+    (synopsis "Dependent Mixture Models")
+    (description "This package fits latent (hidden) Markov models on mixed
+categorical and continuous (time series) data, otherwise known as dependent
+mixture models.")
+    (license license:gpl2+)))
+
 (define-public r-readxl
   (package
     (name "r-readxl")
@@ -1157,6 +1249,36 @@ the embedded @code{RapidXML} C++ library.")
     ;; 'rapidxml' which is Boost.
     (license (list license:gpl3 license:bsd-2 license:boost1.0))))
 
+(define-public r-model4you
+  (package
+    (name "r-model4you")
+    (version "0.9-7")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "model4you" version))
+              (sha256
+               (base32
+                "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-formula" ,r-formula)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-partykit" ,r-partykit)
+       ("r-sandwich" ,r-sandwich)
+       ("r-survival" ,r-survival)))
+    (home-page "https://cran.r-project.org/web/packages/model4you/")
+    (synopsis "Stratified and personalised models based on trees and forests")
+    (description
+     "This package provides procedures for model-based trees for subgroup
+analyses in clinical trials and model-based forests for the estimation and
+prediction of personalised treatment effects.  Currently partitioning of linear
+models, @code{lm()}, generalised linear models, @code{glm()}, and
+Weibull models, @code{survreg()}, are supported.  Advanced plotting functionality is
+supported for the trees and a test for parameter heterogeneity is provided for
+the personalised models.")
+    (license license:gpl2+)))
+
 (define-public r-modelr
   (package
     (name "r-modelr")
@@ -1204,6 +1326,28 @@ and make inference with discrete time and discrete space hidden Markov
 models.")
     (license license:gpl2+)))
 
+(define-public r-hiddenmarkov
+  (package
+   (name "r-hiddenmarkov")
+   (version "1.8-13")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "HiddenMarkov" version))
+            (sha256
+             (base32
+              "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki"))))
+   (build-system r-build-system)
+   (native-inputs
+    `(("gfortran" ,gfortran)))
+   (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/")
+   (synopsis "Hidden markov models for R")
+   (description "This package contains functions for the analysis of Discrete
+Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated
+Poisson Process.  It includes functions for simulation, parameter estimation,
+and the Viterbi algorithm.  The algorithms are based of those of Walter
+Zucchini.")
+   (license license:gpl2+)))
+
 (define-public r-httpuv
   (package
     (name "r-httpuv")
@@ -1307,6 +1451,29 @@ documents that can be converted to HTML files (e.g., R Markdown) under a given
 directory.")
     (license license:expat)))
 
+(define-public r-howmany
+  (package
+    (name "r-howmany")
+    (version "0.3-1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "howmany" version))
+              (sha256
+               (base32
+                "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/howmany/")
+    (synopsis "Lower bound for the number of correct rejections")
+    (description "When testing multiple hypotheses simultaneously, this package
+provides functionality to calculate a lower bound for the number of correct
+rejections (as a function of the number of rejected hypotheses), which holds
+simultaneously -with high probability- for all possible number of rejections.
+As a special case, a lower bound for the total number of false null hypotheses
+can be inferred.  Dependent test statistics can be handled for multiple tests
+of associations.  For independent test statistics, it is sufficient to provide
+a list of p-values.")
+    (license license:gpl2+)))
+
 (define-public r-htmltools
   (package
     (name "r-htmltools")
@@ -2894,6 +3061,26 @@ attaching it.  This is a key part of the @code{devtools} package as it allows
 you to rapidly iterate while developing a package.")
     (license license:gpl3)))
 
+(define-public r-pvclust
+  (package
+   (name "r-pvclust")
+   (version "2.2-0")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "pvclust" version))
+            (sha256
+             (base32
+              "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq"))))
+   (build-system r-build-system)
+   (home-page "https://github.com/shimo-lab/pvclust")
+   (synopsis
+    "Hierarchical clustering with P-values via multiscale bootstrap resampling")
+   (description "This package provides an implementation of multiscale bootstrap
+resampling for assessing the uncertainty in hierarchical cluster analysis.  It
+provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)
+value for each cluster in a dendrogram.")
+   (license license:gpl2+)))
+
 (define-public r-rcpp
   (package
     (name "r-rcpp")
@@ -2939,6 +3126,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
 safely be interrupted from R.")
     (license license:expat)))
 
+(define-public r-rcppnumerical
+  (package
+    (name "r-rcppnumerical")
+    (version "0.4-0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "RcppNumerical" version))
+              (sha256
+               (base32
+                "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)))
+    (home-page "https://github.com/yixuan/RcppNumerical")
+    (synopsis"Numerical computing libraries integration with @code{Rcpp}")
+    (description "This package provides a collection of libraries for numerical
+computing (numerical integration, optimization, etc.) and their integration
+with @code{Rcpp}.")
+    (license license:gpl2+)))
+
 (define-public r-bindr
   (package
     (name "r-bindr")
@@ -3288,6 +3496,25 @@ statistical functions and other utilities to ease their usage.")
 quantities.")
     (license license:expat)))
 
+(define-public r-princurve
+  (package
+   (name "r-princurve")
+   (version "2.1.6")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "princurve" version))
+            (sha256
+             (base32
+              "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-rcpp" ,r-rcpp)))
+   (home-page "https://github.com/rcannood/princurve")
+   (synopsis "Fit a principal curve in arbitrary dimension")
+   (description "This package provides procedures for fitting a principal
+curve to a data matrix in arbitrary dimensions.")
+   (license license:gpl2)))
+
 (define-public r-reshape
   (package
     (name "r-reshape")
@@ -3584,14 +3811,14 @@ which should be seen for details.")
 (define-public r-extremes
   (package
     (name "r-extremes")
-    (version "2.1")
+    (version "2.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "extRemes" version))
        (sha256
         (base32
-         "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
+         "00ps7yggp89sx1j0w6c8dk0la3k95rwjv1iz7rdfqy7i46xjf6as"))))
     (properties `((upstream-name . "extRemes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3653,13 +3880,13 @@ by Li, Brown, Huang, and Bickel")
 (define-public r-inline
   (package
     (name "r-inline")
-    (version "0.3.18")
+    (version "0.3.19")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "inline" version))
               (sha256
                (base32
-                "0fpcfwbhfg1lhkqc0gdqv2sq64r3ljld7piy34vv0nimq30xi2fc"))))
+                "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/inline")
     (synopsis "Functions to inline C, C++, Fortran function calls from R")
@@ -3843,14 +4070,14 @@ functions from LINPACK.")
 (define-public r-fitdistrplus
   (package
     (name "r-fitdistrplus")
-    (version "1.1-3")
+    (version "1.1-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fitdistrplus" version))
        (sha256
         (base32
-         "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
+         "1p9rvvh05zqb9vzhcyzdh7i8lbmb53nj8nyn0gqcmp7wafg9cd1f"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
@@ -5058,6 +5285,44 @@ Friendly and is now the main support package for a new book, \"Discrete Data
 Analysis with R\" by Michael Friendly and David Meyer (2015).")
     (license license:gpl2)))
 
+(define-public r-vcfr
+  (package
+   (name "r-vcfr")
+   (version "1.12.0")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "vcfR" version))
+            (sha256
+             (base32
+              "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx"))))
+   (build-system r-build-system)
+   (native-inputs
+    `(("r-knitr" ,r-knitr)))
+   (inputs
+    `(("zlib" ,zlib)))
+   (propagated-inputs
+    `(("r-ape" ,r-ape)
+      ("r-dplyr" ,r-dplyr)
+      ("r-magrittr" ,r-magrittr)
+      ("r-memuse" ,r-memuse)
+      ("r-pinfsc50" ,r-pinfsc50)
+      ("r-rcpp" ,r-rcpp)
+      ("r-stringr" ,r-stringr)
+      ("r-tibble" ,r-tibble)
+      ("r-vegan" ,r-vegan)
+      ("r-viridislite" ,r-viridislite)))
+   (home-page "https://github.com/knausb/vcfR")
+   (synopsis "Manipulate and visualize VCF data")
+   (description "This package facilitates easy manipulation of variant call
+format (VCF) data.  Functions are provided to rapidly read from and write to
+VCF files.  Once VCF data is read into R, a parser function extracts matrices
+of data.  This information can then be used for quality control or other
+purposes.  Additional functions provide visualization of genomic data.  Once
+processing is complete data may be written to a VCF file.  It also may be
+converted into other popular R objects.  This package provides a link between
+VCF data and familiar R software.")
+   (license license:gpl3)))
+
 (define-public r-ica
   (package
     (name "r-ica")
@@ -5535,6 +5800,25 @@ columns of data using the full range of colours provided by modern
 terminals.")
     (license license:gpl3)))
 
+(define-public r-pinfsc50
+  (package
+   (name "r-pinfsc50")
+   (version "1.2.0")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "pinfsc50" version))
+            (sha256
+             (base32
+              "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd"))))
+   (build-system r-build-system)
+   (home-page "https://cran.r-project.org/web/packages/pinfsc50/")
+   (synopsis "Genomic data for the plant pathogen Phytophthora infestans")
+   (description "This package contains genomic data for the plant pathogen
+Phytophthora infestans.  It includes a variant file, a sequence file and an
+annotation file.  This package is intended to be used as example data for
+packages that work with genomic data.")
+   (license license:gpl2+)))
+
 (define-public r-uuid
   (package
     (name "r-uuid")
@@ -5557,14 +5841,14 @@ terminals.")
 (define-public r-tinytex
   (package
     (name "r-tinytex")
-    (version "0.31")
+    (version "0.32")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tinytex" version))
        (sha256
         (base32
-         "04a3ncaxix30n9m73slpsn1idxv7j1f7fy3nhxpvkk514x9rgg0p"))))
+         "17y20kb5xgmz77n4rrkqmcm0cnjwfi4mn84h6zabij76b8cjiykh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-xfun" ,r-xfun)))
@@ -6280,6 +6564,30 @@ fixed values.  Other functions include a custom @code{geom}, and helper
 functions to enforce symmetric scales or add tags to facetted plots.")
     (license license:gpl3)))
 
+(define-public r-heatmap3
+  (package
+    (name "r-heatmap3")
+    (version "1.1.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "heatmap3" version))
+       (sha256
+        (base32
+         "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-fastcluster" ,r-fastcluster)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://cran.r-project.org/web/packages/heatmap3/")
+    (synopsis "Improved heatmap package")
+    (description
+     "This package provides an improved heatmap package.  It is completely
+compatible with the original R function @code{heatmap}, and provides more
+powerful and convenient features.")
+    (license license:gpl2+)))
+
 (define-public r-heatmaply
   (package
     (name "r-heatmaply")
@@ -6561,14 +6869,14 @@ and within plot factors interact.")
 (define-public r-signal
   (package
     (name "r-signal")
-    (version "0.7-6")
+    (version "0.7-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "signal" version))
        (sha256
         (base32
-         "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
+         "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-mass" ,r-mass)))
     (native-inputs `(("gfortran" ,gfortran)))
@@ -6948,14 +7256,14 @@ misclassification probabilities of different models.")
 (define-public r-zip
   (package
     (name "r-zip")
-    (version "2.1.1")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "zip" version))
        (sha256
         (base32
-         "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
+         "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz"))))
     (build-system r-build-system)
     (home-page "https://github.com/gaborcsardi/zip")
     (synopsis "Cross-platform Zip compression")
@@ -7882,14 +8190,14 @@ steps and provides ggplot2-based elegant data visualization.")
 (define-public r-fansi
   (package
     (name "r-fansi")
-    (version "0.4.2")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fansi" version))
        (sha256
         (base32
-         "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2"))))
+         "0kx5kjhr8dvqz1mq1zkijkgp29jv8b0irm1xplx1d74n2v1zh6wx"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr))) ; for vignettes
@@ -8064,14 +8372,14 @@ implemented in bibutils.")
 (define-public r-rdpack
   (package
     (name "r-rdpack")
-    (version "2.1.1")
+    (version "2.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rdpack" version))
        (sha256
         (base32
-         "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb"))))
+         "0s51c5fw1ka75b8cxk5bh27h6wcy5169yl93sjlxji2k27n9fj3i"))))
     (properties `((upstream-name . "Rdpack")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8316,14 +8624,14 @@ other add-on packages.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.14.0")
+    (version "0.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "1zkifkj2qg9vdv26z4qvi81qv9l1cqyrq3ihdpacpax80plkgdln"))))
+         "0af15kqz4kiyi5p4qi748hvdw462vdwigzyykh1k7vj6gacn2xqf"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)))
@@ -8913,13 +9221,13 @@ based on index arrays and simple triplet representations, respectively.")
 (define-public r-manipulatewidget
   (package
     (name "r-manipulatewidget")
-    (version "0.10.1")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "manipulateWidget" version))
        (sha256
-        (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
+        (base32 "0iysgl6ab8fvg1xxdx6hr3swqwbkfqzjkk4x5sbvmawbl2a395gj"))))
     (properties
      `((upstream-name . "manipulateWidget")))
     (build-system r-build-system)
@@ -8931,7 +9239,10 @@ based on index arrays and simple triplet representations, respectively.")
        ("r-knitr" ,r-knitr)
        ("r-miniui" ,r-miniui)
        ("r-shiny" ,r-shiny)
+       ("r-shinyjs" ,r-shinyjs)
        ("r-webshot" ,r-webshot)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
     (synopsis "Add even more interactivity to interactive charts")
     (description
@@ -10261,14 +10572,14 @@ Hothorn, Westfall, 2010, CRC Press).")
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "07iw3faprf98mncymbjbmfm2yi294yiwdg30xlql5sfx12qbf6r0"))))
+         "02sh1q6f2ik56w348pfkg4a8jvdn3a31r7d8mzg7zq3sv7lmvqwl"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-estimability" ,r-estimability)
@@ -10497,14 +10808,14 @@ differentiation.")
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.9.0")
+    (version "0.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "0msr24ymnazpaz8s9qs5v3xn1i9984p98lr9x4qq9cxgx34rm9h0"))))
+         "1qr51mag5wf44h4sygkn5arsirpqdanf039cg6fxmyw83k51fi2v"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10581,14 +10892,14 @@ results using @code{ggplot2}.")
 (define-public r-effectsize
   (package
     (name "r-effectsize")
-    (version "0.4.4-1")
+    (version "0.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "effectsize" version))
        (sha256
         (base32
-         "02rwf3lxnzgc8yh0wridsc6lqr9s6v0cqzbk4biwnr494rvs46zb"))))
+         "0rp0r75p8q467lmrsr1gl9wjpib9jz7ksx5rm6c7q2lfg9b9zrjf"))))
     (properties `((upstream-name . "effectsize")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10608,13 +10919,13 @@ conversion of indices such as Cohen's d, r, odds, etc.")
 (define-public r-sjplot
   (package
     (name "r-sjplot")
-    (version "2.8.7")
+    (version "2.8.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjPlot" version))
        (sha256
-        (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0"))))
+        (base32 "050aarycgzy1n8ad67pj09s8k7s7xk6dicg0kjg0ivlkyyq0shqz"))))
     (properties `((upstream-name . "sjPlot")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11187,14 +11498,14 @@ the interfaces between R and C++.")
 (define-public r-mvabund
   (package
     (name "r-mvabund")
-    (version "4.1.9")
+    (version "4.1.12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mvabund" version))
        (sha256
         (base32
-         "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30"))))
+         "107pwv2bwird1a98chcnbld2wqj9prkf4pkncyrrp304zpdkkby1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
@@ -11301,21 +11612,21 @@ al. (2016)).")
 (define-public r-weights
   (package
     (name "r-weights")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "weights" version))
        (sha256
         (base32
-         "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
+         "1sq8ls5idspddn8m2c8n2107lgx53kbach8vgjrhqx1mc6xfvrvw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-gdata" ,r-gdata)
        ("r-hmisc" ,r-hmisc)
+       ("r-lme4" ,r-lme4)
        ("r-mice" ,r-mice)))
-    (home-page
-     "https://cran.r-project.org/web/packages/weights/")
+    (home-page "https://cran.r-project.org/web/packages/weights/")
     (synopsis "Weighting and weighted statistics")
     (description "This package Provides a variety of functions for producing
 simple weighted statistics, such as weighted Pearson's correlations, partial
@@ -11531,13 +11842,13 @@ isosurfaces.")
 (define-public r-ks
   (package
     (name "r-ks")
-    (version "1.12.0")
+    (version "1.13.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ks" version))
        (sha256
-        (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
+        (base32 "0zi7yixz3hvqvb5fxipkxprk5p4irr61csd3k6scsxqyhrb5ffls"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-fnn" ,r-fnn)
@@ -11548,7 +11859,8 @@ isosurfaces.")
        ("r-mgcv" ,r-mgcv)
        ("r-multicool" ,r-multicool)
        ("r-mvtnorm" ,r-mvtnorm)
-       ("r-plot3d" ,r-plot3d)))
+       ("r-plot3d" ,r-plot3d)
+       ("r-pracma" ,r-pracma)))
     (home-page "https://www.mvstat.net/tduong/")
     (synopsis "Kernel smoothing")
     (description
@@ -11997,13 +12309,13 @@ maps.")
 (define-public r-tidytree
   (package
     (name "r-tidytree")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytree" version))
        (sha256
-        (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
+        (base32 "0bqsb0zplkqkx2mp8kpanadkds4kwwvdrc07lp0qzwqqzaxq5xa3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ape" ,r-ape)
@@ -12385,6 +12697,89 @@ Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
 Touzet and Varre (2007).")
     (license license:gpl2)))
 
+(define-public r-rncl
+  (package
+    (name "r-rncl")
+    (version "0.8.4")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "rncl" version))
+              (sha256
+               (base32
+                "0ss9jqrvv7bhvl5j74cjrp8r866d9dlavrbbfscwz3mhkgfx06bb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-progress" ,r-progress)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/fmichonneau/rncl")
+    (synopsis "Interface to the Nexus class library")
+    (description "This package provides an interface to the Nexus class
+library which allows parsing of NEXUS, Newick and other phylogenetic tree
+ file formats.  It provides elements of the file that can be used to build
+ phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s
+@code{phylo4(d)}.  This functionality is demonstrated with
+@code{read_newick_phylo()} and @code{read_nexus_phylo()}.")
+    (license license:bsd-2)))
+
+(define-public r-phylobase
+  (package
+    (name "r-phylobase")
+    (version "0.8.10")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "phylobase" version))
+              (sha256
+               (base32
+                "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ade4" ,r-ade4)
+       ("r-ape" ,r-ape)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rncl" ,r-rncl)
+       ("r-rnexml" ,r-rnexml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/fmichonneau/phylobase")
+    (synopsis "Base package for phylogenetic structures and comparative data")
+    (description "This package provides a base @code{S4} class for comparative
+methods, incorporating one or more trees and trait data.")
+    (license license:gpl2+)))
+
+(define-public r-rnexml
+  (package
+    (name "r-rnexml")
+    (version "2.4.5")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "RNeXML" version))
+              (sha256
+               (base32
+                "1wsl4xq9w5bp3wk69dw57bg0qcw1vs6ajwya4p0w1r00ck5pwrib"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-dplyr" ,r-dplyr)
+       ("r-httr" ,r-httr)
+       ("r-lazyeval" ,r-lazyeval)
+       ("r-plyr" ,r-plyr)
+       ("r-reshape2" ,r-reshape2)
+       ("r-stringi" ,r-stringi)
+       ("r-stringr" ,r-stringr)
+       ("r-tidyr" ,r-tidyr)
+       ("r-uuid" ,r-uuid)
+       ("r-xml" ,r-xml)
+       ("r-xml2" ,r-xml2)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://docs.ropensci.org/RNeXML/")
+    (synopsis "Semantically rich I/O for the NeXML Format")
+    (description "This package provides access to phyloinformatic data in
+NeXML format.  The package should add new functionality to R such as the
+possibility to manipulate NeXML objects in more various and refined way
+and compatibility with @code{ape} objects.")
+    (license license:bsd-3)))
+
 (define-public r-rnifti
   (package
     (name "r-rnifti")
@@ -13504,6 +13899,23 @@ Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
     (license license:gpl2+)))
 
+(define-public r-locfdr
+  (package
+    (name "r-locfdr")
+    (version "1.1-8")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "locfdr" version))
+              (sha256
+               (base32
+                "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/locfdr/")
+    (synopsis "Computes local false discovery rates")
+    (description "This package can be used to compute local false
+discovery rates.")
+    (license license:gpl2)))
+
 (define-public r-longitudinal
   (package
     (name "r-longitudinal")
@@ -15493,14 +15905,26 @@ datum transformations.")
 (define-public r-spdep
   (package
     (name "r-spdep")
-    (version "1.1-7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "spdep" version))
-       (sha256
-        (base32
-         "0sg417d95paww625663lgmk6jwhs88djqzc96gbs1hxazlf77qb1"))))
+    (version "1.1-8")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "spdep" version))
+              (sha256
+               (base32
+                "1k82vx58kpn0fwgcpxq2jc3qfffl8wzbgr4cdkxihrfk28kkqh7l"))
+              (snippet
+               '(for-each delete-file '("inst/doc/nb_igraph.html"
+                                        "inst/doc/nb_igraph.R"
+                                        "inst/doc/nb_igraph.Rmd"
+                                        "inst/doc/sids.html"
+                                        "inst/doc/sids.R"
+                                        "inst/doc/nb.html"
+                                        "inst/doc/nb.R"
+                                        "inst/doc/CO69.html"
+                                        "inst/doc/CO69.R"
+                                        "inst/doc/nb_sf.html"
+                                        "inst/doc/nb_sf.R"
+                                        "inst/doc/nb_sf.Rmd")))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-boot" ,r-boot)
@@ -17249,6 +17673,116 @@ making it possible to download files over HTTPS across platforms.  The
 external dependencies.  This package has is implemented purely in R.")
     (license license:gpl2)))
 
+(define-public r-aplot
+  (package
+    (name "r-aplot")
+    (version "0.0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "aplot" version))
+       (sha256
+        (base32
+         "08kqrm9r57l8zgij897wpp428l4i50qfhp7y78r3pk5pjz37bsan"))))
+    (properties `((upstream-name . "aplot")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-magrittr" ,r-magrittr)
+       ("r-patchwork" ,r-patchwork)))
+    (home-page "https://github.com/YuLab-SMU/aplot")
+    (synopsis "Decorate a ggplot with associated information")
+    (description
+     "Users may want to align plots with associated information that requires
+axes to be exactly matched in subplots, e.g. hierarchical clustering with a
+heatmap.  This package provides utilities to align associated subplots to a
+main plot at different sides (left, right, top and bottom) with axes exactly
+matched.")
+    (license license:artistic2.0)))
+
+(define-public r-ggnewscale
+  (package
+    (name "r-ggnewscale")
+    (version "0.4.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggnewscale" version))
+       (sha256
+        (base32
+         "1hjysfagd2lqy8yivqq9q7l6hbvyq8kasw3zqh5fk9xn18ikc702"))))
+    (properties `((upstream-name . "ggnewscale")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)))
+    (home-page "https://cran.r-project.org/package=ggnewscale")
+    (synopsis "Multiple fill and color scales in ggplot2")
+    (description
+     "This package lets you use multiple fill and color scales in ggplot2.")
+    (license license:gpl3)))
+
+(define-public r-ggpointdensity
+  (package
+    (name "r-ggpointdensity")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggpointdensity" version))
+       (sha256
+        (base32
+         "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy"))))
+    (properties
+     `((upstream-name . "ggpointdensity")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)))
+    (home-page "https://github.com/LKremer/ggpointdensity")
+    (synopsis "Cross between a 2D density plot and a scatter plot")
+    (description
+     "This package provides a cross between a 2D density plot and a scatter
+plot, implemented as a ggplot2 @code{geom}.  Points in the scatter plot are
+colored by the number of neighboring points.  This is useful to visualize the
+2D-distribution of points in case of overplotting.")
+    (license license:gpl3)))
+
+(define-public r-arrow
+  (package
+    (name "r-arrow")
+    (version "4.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "arrow" version))
+       (sha256
+        (base32
+         "19kzfjxp90ybi1px3r93mfx59nqmnagxr4g73y7iby5blwl1bblc"))))
+    (properties `((upstream-name . "arrow")))
+    (build-system r-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-assertthat" ,r-assertthat)
+       ("r-bit64" ,r-bit64)
+       ("r-cpp11" ,r-cpp11)
+       ("r-purrr" ,r-purrr)
+       ("r-r6" ,r-r6)
+       ("r-rlang" ,r-rlang)
+       ("r-tidyselect" ,r-tidyselect)
+       ("r-vctrs" ,r-vctrs)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/apache/arrow/")
+    (synopsis "R integration to Apache Arrow")
+    (description
+     "Apache Arrow is a cross-language development platform for in-memory
+data.  It specifies a standardized language-independent columnar memory format
+for flat and hierarchical data, organized for efficient analytic operations on
+modern hardware.  This package provides an R interface to the Arrow C++
+library.")
+    (license license:asl2.0)))
+
 (define-public r-rex
   (package
     (name "r-rex")
@@ -17709,14 +18243,14 @@ been used in the call to @code{aov}.")
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "2.2.0")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "1qnjbhilv4jfmwqxfi9xc5ysrh8gr84a2a5imjfci7d1n3zcnryn"))))
+         "184mzby1giismhx4brvrdfl5n5kialyvv8ik18blhchvpy145cwf"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17765,14 +18299,14 @@ annotated biological functions.")
 (define-public r-plot3d
   (package
     (name "r-plot3d")
-    (version "1.3")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "plot3D" version))
        (sha256
         (base32
-         "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
+         "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
     (properties `((upstream-name . "plot3D")))
     (build-system r-build-system)
     (propagated-inputs `(("r-misc3d" ,r-misc3d)))
@@ -18103,14 +18637,14 @@ computed using the L1 (Manhattan, taxicab) metric.")
 (define-public r-leiden
   (package
     (name "r-leiden")
-    (version "0.3.7")
+    (version "0.3.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "leiden" version))
        (sha256
         (base32
-         "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
+         "0sv0j4sgpz8z65vhbpmaglg878jhq52srzf5rpw4vbsbys2807w1"))))
     (properties `((upstream-name . "leiden")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18491,14 +19025,14 @@ in pipelines.")
 (define-public r-parameters
   (package
     (name "r-parameters")
-    (version "0.13.0")
+    (version "0.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parameters" version))
        (sha256
         (base32
-         "17dlwx9hrl6z2il14nxji0snwsf4sfbp3mv33jbpcw13sani1q81"))))
+         "03x2h8izbpz9cq25i0a6dh99m26a9isgpv4kxsfkx97qzlh9cd67"))))
     (properties `((upstream-name . "parameters")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19645,6 +20179,31 @@ introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
     (license license:bsd-3)))
 
+(define-public r-rnmf
+  (package
+   (name "r-rnmf")
+   (version "0.5.0")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "rNMF" version))
+            (sha256
+             (base32
+              "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-knitr" ,r-knitr)
+      ("r-nnls" ,r-nnls)))
+   (home-page "https://cran.r-project.org/web/packages/rNMF/")
+   (synopsis "Robust nonnegative matrix factorization")
+   (description
+    "This package provides an implementation of robust nonnegative matrix
+factorization (rNMF).  The rNMF algorithm decomposes a nonnegative high
+dimension data matrix into the product of two low rank nonnegative matrices,
+while detecting and trimming outliers.  The main function is @code{rnmf()}.
+The package also includes a visualization tool, @code{see()}, that arranges
+and prints vectorized images.")
+   (license license:gpl2+)))
+
 (define-public r-randtoolbox
   (package
     (name "r-randtoolbox")
@@ -20353,6 +20912,23 @@ modeling often used in @dfn{analytical customer relationship
 management} (aCRM).")
     (license license:gpl2+)))
 
+(define-public r-tree
+  (package
+   (name "r-tree")
+   (version "1.0-40")
+   (source (origin
+            (method url-fetch)
+            (uri (cran-uri "tree" version))
+            (sha256
+             (base32
+              "1rr6ws62j9h36f3nl713f8h3ndkh95mv46l055jvgmby5lw1dazz"))))
+   (build-system r-build-system)
+   (home-page "https://cran.r-project.org/web/packages/tree/")
+   (synopsis "Classification and regression trees")
+   (description "This package provides procedures to work with classification
+and regression trees.")
+   (license license:gpl2+)))
+
 (define-public r-treeclust
   (package
     (name "r-treeclust")
@@ -20563,14 +21139,14 @@ allowed.")
 (define-public r-gdina
   (package
     (name "r-gdina")
-    (version "2.8.0")
+    (version "2.8.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "GDINA" version))
        (sha256
         (base32
-         "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
+         "08cdjp4mqn81j3wa770v7n8zkslys9jqqb3d3c09dkfmgdk6hga4"))))
     (properties `((upstream-name . "GDINA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21026,14 +21602,14 @@ API; see the package vignette for details.")
 (define-public r-actuar
   (package
     (name "r-actuar")
-    (version "3.1-2")
+    (version "3.1-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "actuar" version))
        (sha256
         (base32
-         "0gaqm8bkjly2b1jkr1nqnxlp5vqvfpj0a4jd70jv4f9ndlif676y"))))
+         "0m9b4787a866cddf1skjz6634237dvg1i5qyqss4sgvcrbmx3hw0"))))
     (properties `((upstream-name . "actuar")))
     (build-system r-build-system)
     (propagated-inputs `(("r-expint" ,r-expint)))
@@ -21360,14 +21936,14 @@ cluster stability.")
 (define-public r-biclust
   (package
     (name "r-biclust")
-    (version "2.0.2")
+    (version "2.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "biclust" version))
        (sha256
         (base32
-         "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
+         "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp"))))
     (properties `((upstream-name . "biclust")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21922,14 +22498,14 @@ both exclusive and shared locking.")
 (define-public r-archivist
   (package
     (name "r-archivist")
-    (version "2.3.5")
+    (version "2.3.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "archivist" version))
        (sha256
         (base32
-         "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
+         "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9"))))
     (properties `((upstream-name . "archivist")))
     (build-system r-build-system)
     (propagated-inputs
@@ -22094,14 +22670,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
 (define-public r-forecast
   (package
     (name "r-forecast")
-    (version "8.14")
+    (version "8.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "forecast" version))
        (sha256
         (base32
-         "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s"))))
+         "0x4ij55sb45qnwba3bybs50vsvv82q3j8p47xmbv959h13nsnfn7"))))
     (properties `((upstream-name . "forecast")))
     (build-system r-build-system)
     (propagated-inputs
@@ -23076,14 +23652,14 @@ and reproducible way.")
 (define-public r-rsconnect
   (package
     (name "r-rsconnect")
-    (version "0.8.17")
+    (version "0.8.18")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rsconnect" version))
        (sha256
         (base32
-         "0cd2bpc22jam1qxn6yg7yr7xdhsm0jgnm5bm2f3vg5b3c96plxk4"))))
+         "01bj16iggj5fggfa7n312458p8xg30zx2vzfkd8jqcchnbrphfvl"))))
     (properties `((upstream-name . "rsconnect")))
     (build-system r-build-system)
     (propagated-inputs
@@ -24880,6 +25456,26 @@ theory; see @url{Strumbel and Kononenko (2014),
 doi.org/10.1007/s10115-013-0679-x} for details.")
     (license license:gpl2+)))
 
+(define-public r-memuse
+  (package
+    (name "r-memuse")
+    (version "4.1-0")
+    (source (origin
+             (method url-fetch)
+             (uri (cran-uri "memuse" version))
+             (sha256
+              (base32
+               "1bbjp8y0ji71956fbaxiil7ynq2nkmmgz7i9xps83m3bbp5d3mjq"))))
+    (properties `((upstream-name . "memuse")))
+    (build-system r-build-system)
+    (home-page "https://github.com/shinra-dev/memuse")
+    (synopsis "Memory Estimation Utilities")
+    (description
+      "This package provides procedures to answer the following questions:
+How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is
+your current R session using? How much ram do you even have?")
+    (license license:bsd-2)))
+
 (define-public r-metrics
   (package
     (name "r-metrics")
@@ -25286,17 +25882,41 @@ maximums, many t, F and G-square tests, many regressions (normal, logistic,
 Poisson), are some of the many fast functions.")
     (license license:gpl2+)))
 
+(define-public r-rffc
+  (package
+   (name "r-rffc")
+   (version "1.0")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://download.r-forge.r-project.org/src/contrib/"
+                  "rfFC_" version ".tar.gz"))
+            (sha256
+             (base32
+              "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g"))))
+   (build-system r-build-system)
+   (propagated-inputs
+    `(("r-randomforest",r-randomforest)))
+   (home-page "https://r-forge.r-project.org/projects/rffc/")
+   (synopsis "Random Forest Feature Contributions")
+   (description "This package provides functions for extracting feature
+contributions from a random forest model from package @code{randomForest}.
+Feature contributions provide detailed information about the relationship
+between data variables and the predicted value returned by random forest
+model.")
+   (license license:gpl2)))
+
 (define-public r-clusterr
   (package
     (name "r-clusterr")
-    (version "1.2.4")
+    (version "1.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ClusterR" version))
        (sha256
         (base32
-         "01vgr1mpm7l1lyhril5hm1l72aicqc4iwb0b15ypijb6hwkv7g47"))))
+         "1fsb9pzs1paw1cbyr5a56lfh8h2d50232p6isk0xg5sl110ql7kx"))))
     (properties `((upstream-name . "ClusterR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25412,6 +26032,35 @@ so that natural sort function arranges a character vector by their numbers,
 not digit characters.")
    (license license:bsd-3)))
 
+(define-public r-visdat
+  (package
+    (name "r-visdat")
+    (version "0.5.3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "visdat" version))
+              (sha256
+               (base32
+                "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-glue" ,r-glue)
+       ("r-magrittr" ,r-magrittr)
+       ("r-purrr" ,r-purrr)
+       ("r-readr" ,r-readr)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://visdat.njtierney.com/")
+    (synopsis "Preliminary Visualisation of Data")
+    (description "This package provides procedures to create preliminary exploratory
+data visualisations of an entire dataset to identify problems or unexpected features
+using @code{ggplot2}.")
+    (license license:expat)))
+
 (define-public r-muhaz
   (package
     (name "r-muhaz")
@@ -26336,14 +26985,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
 (define-public r-parsnip
   (package
     (name "r-parsnip")
-    (version "0.1.5")
+    (version "0.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "parsnip" version))
        (sha256
         (base32
-         "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06"))))
+         "0qhdh2xdswqy94f4gkdxi1iqm0k794p9y8sdh6mgbd1a86c8ngfs"))))
     (properties `((upstream-name . "parsnip")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26351,6 +27000,7 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
        ("r-generics" ,r-generics)
        ("r-globals" ,r-globals)
        ("r-glue" ,r-glue)
+       ("r-lifecycle" ,r-lifecycle)
        ("r-magrittr" ,r-magrittr)
        ("r-prettyunits" ,r-prettyunits)
        ("r-purrr" ,r-purrr)
@@ -26795,13 +27445,13 @@ other R users.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "4.0.1")
+    (version "4.0.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p"))))
+                "1b1wyj4dxjn0hfg09l8z282grdgwgah0czs7pn2ian455x0dphng"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26923,14 +27573,14 @@ rate speciation and extinction.")
 (define-public r-calculus
   (package
     (name "r-calculus")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "calculus" version))
        (sha256
         (base32
-         "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj"))))
+         "0m9cjc3bqv88vrrj51kd7c7xnczka5w9q0ln4l4nk514gvlr79bn"))))
     (properties `((upstream-name . "calculus")))
     (build-system r-build-system)
     (propagated-inputs
@@ -27837,14 +28487,14 @@ in same length matches).")
 (define-public r-textshape
   (package
     (name "r-textshape")
-    (version "1.7.1")
+    (version "1.7.3")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "textshape" version))
         (sha256
           (base32
-            "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa"))))
+            "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds"))))
     (properties `((upstream-name . "textshape")))
     (build-system r-build-system)
     (propagated-inputs
@@ -28629,35 +29279,6 @@ indicator, a quantitative variable or a survival time.")
     ;; Any version of the LGPL
     (license license:lgpl3+)))
 
-(define-public r-samr
-  (package
-    (name "r-samr")
-    (version "3.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "samr" version))
-       (sha256
-        (base32
-         "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
-    (properties `((upstream-name . "samr")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-gsa" ,r-gsa)
-       ("r-impute" ,r-impute)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-openxlsx" ,r-openxlsx)
-       ("r-shiny" ,r-shiny)
-       ("r-shinyfiles" ,r-shinyfiles)))
-    (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "https://statweb.stanford.edu/~tibs/SAM/")
-    (synopsis "Significance analysis of Microarrays")
-    (description
-     "This is a package for significance analysis of Microarrays for
-differential expression analysis, RNAseq data and related problems.")
-    ;; Any version of the LGPL
-    (license license:lgpl3+)))
-
 (define-public r-randomforestsrc
   (package
     (name "r-randomforestsrc")
@@ -28683,3 +29304,72 @@ quantile regression and solutions for class imbalanced data.  It provides a
 fast interface using subsampling and confidence regions for variable
 importance.")
     (license license:gpl3+)))
+
+(define-public r-contfrac
+  (package
+    (name "r-contfrac")
+    (version "1.1-12")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "contfrac" version))
+        (sha256
+          (base32
+            "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm"))))
+    (properties `((upstream-name . "contfrac")))
+    (build-system r-build-system)
+    (home-page
+      "https://github.com/RobinHankin/contfrac")
+    (synopsis "Continued Fractions")
+    (description
+      "Various utilities for evaluating continued fractions.")
+    (license license:gpl2)))
+
+(define-public r-elliptic
+  (package
+    (name "r-elliptic")
+    (version "1.4-0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "elliptic" version))
+        (sha256
+          (base32
+            "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn"))))
+    (properties `((upstream-name . "elliptic")))
+    (build-system r-build-system)
+    (inputs `(("pari-gp" ,pari-gp)))
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (home-page
+      "https://github.com/RobinHankin/elliptic")
+    (synopsis
+      "Weierstrass and Jacobi Elliptic Functions")
+    (description
+      "A suite of elliptic and related functions including Weierstrass and
+Jacobi forms.  Also includes various tools for manipulating and visualizing
+complex functions.")
+    (license license:gpl2)))
+
+(define-public r-hypergeo
+  (package
+    (name "r-hypergeo")
+    (version "1.2-13")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "hypergeo" version))
+        (sha256
+          (base32
+            "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd"))))
+    (properties `((upstream-name . "hypergeo")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-contfrac" ,r-contfrac)
+        ("r-desolve" ,r-desolve)
+        ("r-elliptic" ,r-elliptic)))
+    (home-page
+      "https://cran.r-project.org/web/packages/hypergeo/")
+    (synopsis "The Gauss Hypergeometric Function")
+    (description
+      "The Gaussian hypergeometric function for complex numbers.")
+    (license license:gpl2)))
diff --git a/gnu/packages/crates-graphics.scm b/gnu/packages/crates-graphics.scm
index e5719f97e4..bc47bf1287 100644
--- a/gnu/packages/crates-graphics.scm
+++ b/gnu/packages/crates-graphics.scm
@@ -10,6 +10,7 @@
 ;;; Copyright © 2020 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2020, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
+;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,6 +33,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (gnu packages)
+  #:use-module (gnu packages assembly)
   #:use-module (gnu packages crates-io)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages llvm)
@@ -269,6 +271,38 @@ the term library to handle the ANSI nonsense and hence it works on Windows,
 Mac, and Unix.")
     (license (list license:asl2.0 license:expat))))
 
+(define-public rust-avif-parse-0.13
+  (package
+    (name "rust-avif-parse")
+    (version "0.13.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "avif-parse" version))
+       (file-name
+        (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1vylrjq77mpl6flmd85j5f2qimh6vjn03syvq8agb62x56khm0xj"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs
+       (("rust-bitreader" ,rust-bitreader-0.3)
+        ("rust-byteorder" ,rust-byteorder-1)
+        ("rust-fallible-collections" ,rust-fallible-collections-0.4)
+        ("rust-log" ,rust-log-0.4)
+        ("rust-static-assertions" ,rust-static-assertions-1))
+       #:cargo-development-inputs
+       (("rust-env-logger" ,rust-env-logger-0.8)
+        ("rust-walkdir" ,rust-walkdir-2))))
+    (home-page "https://github.com/kornelski/avif-parse")
+    (synopsis "Parser for AVIF image files")
+    (description "This AVIF parser allows extracting the AV1 payload and alpha
+channel metadata out of AVIF image files.  The parser is a fork of Mozilla's
+MP4 parser used in Firefox, so it's designed to be robust and safely handle
+untrusted data.")
+    (license license:mpl2.0)))
+
 (define-public rust-avif-serialize-0.6
   (package
     (name "rust-avif-serialize")
@@ -1915,75 +1949,6 @@ interactive applications.")
         ("rust-glob" ,rust-glob-0.2)
         ("rust-term" ,rust-term-0.4))))))
 
-(define-public rust-rav1e-0.4
-  (package
-    (name "rust-rav1e")
-    (version "0.4.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (crate-uri "rav1e" version))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32 "02cpgzycfgnflnv8sck6ajasa7abfgdzn6b4jv01sf6r21yfipbq"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
-       (("rust-aom-sys" ,rust-aom-sys-0.2)
-        ("rust-arbitrary" ,rust-arbitrary-0.4)
-        ("rust-arg-enum-proc-macro" ,rust-arg-enum-proc-macro-0.3)
-        ("rust-arrayvec" ,rust-arrayvec-0.5)
-        ("rust-assert-cmd" ,rust-assert-cmd-1)
-        ("rust-av-metrics" ,rust-av-metrics-0.6)
-        ("rust-backtrace" ,rust-backtrace-0.3)
-        ("rust-bitstream-io" ,rust-bitstream-io-1)
-        ("rust-byteorder" ,rust-byteorder-1)
-        ("rust-cc" ,rust-cc-1)
-        ("rust-cfg-if" ,rust-cfg-if-1)
-        ("rust-clap" ,rust-clap-2)
-        ("rust-console" ,rust-console-0.14)
-        ("rust-criterion" ,rust-criterion-0.3)
-        ("rust-crossbeam" ,rust-crossbeam-0.8)
-        ("rust-dav1d-sys" ,rust-dav1d-sys-0.3)
-        ("rust-fern" ,rust-fern-0.6)
-        ("rust-image" ,rust-image-0.23)
-        ("rust-interpolate-name" ,rust-interpolate-name-0.2)
-        ("rust-itertools" ,rust-itertools-0.10)
-        ("rust-ivf" ,rust-ivf-0.1)
-        ("rust-libc" ,rust-libc-0.2)
-        ("rust-libfuzzer-sys" ,rust-libfuzzer-sys-0.3)
-        ("rust-log" ,rust-log-0.4)
-        ("rust-nasm-rs" ,rust-nasm-rs-0.2)
-        ("rust-noop-proc-macro" ,rust-noop-proc-macro-0.3)
-        ("rust-num-derive" ,rust-num-derive-0.3)
-        ("rust-num-traits" ,rust-num-traits-0.2)
-        ("rust-paste" ,rust-paste-1)
-        ("rust-pretty-assertions" ,rust-pretty-assertions-0.6)
-        ("rust-rand" ,rust-rand-0.8)
-        ("rust-rand-chacha" ,rust-rand-chacha-0.3)
-        ("rust-rayon" ,rust-rayon-1)
-        ("rust-regex" ,rust-regex-1)
-        ("rust-rust-hawktracer" ,rust-rust-hawktracer-0.7)
-        ("rust-rustc-version" ,rust-rustc-version-0.3)
-        ("rust-scan-fmt" ,rust-scan-fmt-0.2)
-        ("rust-serde" ,rust-serde-1)
-        ("rust-signal-hook" ,rust-signal-hook-0.3)
-        ("rust-simd-helpers" ,rust-simd-helpers-0.1)
-        ("rust-thiserror" ,rust-thiserror-1)
-        ("rust-toml" ,rust-toml-0.5)
-        ("rust-v-frame" ,rust-v-frame-0.2)
-        ("rust-vergen" ,rust-vergen-3)
-        ("rust-wasm-bindgen" ,rust-wasm-bindgen-0.2)
-        ("rust-y4m" ,rust-y4m-0.7))))
-    (home-page "https://github.com/xiph/rav1e")
-    (synopsis "Fast and safe AV1 encoder")
-    (description
-     "@code{rav1e} is an AV1 video encoder.  It is designed to eventually
-cover all use cases, though in its current form it is most suitable for cases
-where libaom (the reference encoder) is too slow.")
-    (license license:bsd-2)))
-
 (define-public rust-ravif-0.6
   (package
     (name "rust-ravif")
@@ -1997,20 +1962,22 @@ where libaom (the reference encoder) is too slow.")
         (base32 "1gyc7w1fz3qdk95cdpkj185dm6lskxfp329xm69waxc565fcz9rx"))))
     (build-system cargo-build-system)
     (arguments
-     `(#:skip-build? #t
-       #:cargo-inputs
+     `(#:cargo-inputs
        (("rust-avif-serialize" ,rust-avif-serialize-0.6)
         ("rust-imgref" ,rust-imgref-1)
         ("rust-loop9" ,rust-loop9-0.1)
         ("rust-num-cpus" ,rust-num-cpus-1)
-        ("rust-rav1e" ,rust-rav1e-0.4)
+        ("rav1e" ,rav1e)
         ("rust-rayon" ,rust-rayon-1)
-        ("rust-rgb" ,rust-rgb-0.8))))
+        ("rust-rgb" ,rust-rgb-0.8))
+       #:cargo-development-inputs
+       (("rust-avif-parse" ,rust-avif-parse-0.13))))
+    (native-inputs
+     `(("nasm" ,nasm)))                 ;for building rav1e
     (home-page "https://lib.rs/ravif")
     (synopsis "Library for encoding images in AVIF format")
-    (description
-     "This package is a rav1e-based pure Rust library for encoding images in
-AVIF format.")
+    (description "This package is a rav1e-based pure Rust library for encoding
+images in AVIF format.")
     (license license:bsd-3)))
 
 (define-public rust-raw-window-handle-0.3
diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm
index c488a769f6..76c1b2f954 100644
--- a/gnu/packages/crates-io.scm
+++ b/gnu/packages/crates-io.scm
author	Maxime Devos <maximedevos@telenet.be>	2021-07-19 11:08:40 +0200
committer	Ludovic Courtès <ludo@gnu.org>	2021-07-23 10:51:57 +0200
commit	d7942ac12ad51615cd43d3debb8b561a503e8fc0 (patch)
tree	25ef7f939eb7dd24d4dca7c8c12af2e1091b5bbc /gnu/packages/patches/audiofile-fix-sign-conversion.patch
parent	93a5e89008af440655527d03d62d4726683a89ac (diff)
download	guix-d7942ac12ad51615cd43d3debb8b561a503e8fc0.tar.gz guix-d7942ac12ad51615cd43d3debb8b561a503e8fc0.zip