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# GNU Guix --- Functional package management for GNU
# Copyright © 2012-2024 Ludovic Courtès <ludo@gnu.org>
# Copyright © 2013 Andreas Enge <andreas@enge.fr>
# Copyright © 2015, 2017 Alex Kost <alezost@gmail.com>
# Copyright © 2016, 2018 Mathieu Lirzin <mthl@gnu.org>
# Copyright © 2016, 2017, 2018, 2019 Mark H Weaver <mhw@netris.org>
# Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
# Copyright © 2017 Leo Famulari <leo@famulari.name>
# Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
# Copyright © 2017, 2020, 2023, 2024 Janneke Nieuwenhuizen <janneke@gnu.org>
# Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
# Copyright © 2018 Nikita <nikita@n0.is>
# Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
# Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
# Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
# Copyright © 2019, 2023 Efraim Flashner <efraim@flashner.co.il>
# Copyright © 2020, 2021, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
# Copyright © 2021 Chris Marusich <cmmarusich@gmail.com>
# Copyright © 2021 Andrew Tropin <andrew@trop.in>
# Copyright © 2023 Clément Lassieur <clement@lassieur.org>
# Copyright © 2023, 2024 Wilko Meyer <w@wmeyer.eu>
# Copyright © 2024 gemmaro <gemmaro.dev@gmail.com>
#
# This file is part of GNU Guix.
#
# GNU Guix is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
#
# GNU Guix is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

MSGMERGE_UPDATE = @MSGMERGE@ --update

bin_SCRIPTS = scripts/guix

# Handle substitution of fully-expanded Autoconf variables.
do_subst = $(SED)					\
  -e 's,[@]GUILE[@],$(GUILE),g'				\
  -e 's,[@]guilemoduledir[@],$(guilemoduledir),g'	\
  -e 's,[@]guileobjectdir[@],$(guileobjectdir),g'	\
  -e 's,[@]abs_top_builddir[@],$(abs_top_builddir),g'	\
  -e 's,[@]localedir[@],$(localedir),g'

scripts/guix: scripts/guix.in Makefile
	$(AM_V_at)rm -f $@ $@-t
	$(AM_V_at)$(MKDIR_P) "$(@D)"
	$(AM_V_GEN)$(do_subst) < "$(srcdir)/$@.in" > "$@-t"
	$(AM_V_at)chmod a+x,a-w "$@-t" && mv -f "$@-t" "$@"

# This is our variant of the 'guile' executable, one that doesn't complain
# about locales.
pkglibexec_PROGRAMS = guile
guile_SOURCES = gnu/packages/aux-files/guile-launcher.c
guile_LDADD   = $(GUILE_LIBS)
guile_CFLAGS  = $(GUILE_CFLAGS)

# Have the 'guix' command refer to our 'guile'.
install-exec-hook:
	$(SED) -i "$(DESTDIR)$(bindir)/guix"				\
	       -e 's,^#![[:graph:]]\+,#!$(pkglibexecdir)/guile,g'

nodist_noinst_SCRIPTS =				\
  pre-inst-env					\
  test-env

# Modules that are not compiled but are installed nonetheless, such as
# build-side modules with unusual dependencies.
MODULES_NOT_COMPILED =				\
  guix/build/po.scm				\
  guix/man-db.scm

include gnu/local.mk
include po/doc/local.mk

MODULES =					\
  guix/base16.scm				\
  guix/base32.scm				\
  guix/base64.scm				\
  guix/ci.scm					\
  guix/cpio.scm					\
  guix/cpu.scm					\
  guix/deprecation.scm				\
  guix/docker.scm	   			\
  guix/records.scm				\
  guix/openpgp.scm				\
  guix/pki.scm					\
  guix/progress.scm				\
  guix/combinators.scm				\
  guix/memoization.scm				\
  guix/utils.scm				\
  guix/sets.scm					\
  guix/modules.scm				\
  guix/download.scm				\
  guix/discovery.scm				\
  guix/android-repo-download.scm		\
  guix/bzr-download.scm            		\
  guix/git-download.scm				\
  guix/hg-download.scm				\
  guix/hash.scm					\
  guix/swh.scm					\
  guix/monads.scm				\
  guix/monad-repl.scm				\
  guix/gexp.scm					\
  guix/profiles.scm				\
  guix/serialization.scm			\
  guix/nar.scm					\
  guix/narinfo.scm				\
  guix/derivations.scm				\
  guix/grafts.scm				\
  guix/repl.scm					\
  guix/rpm.scm					\
  guix/transformations.scm			\
  guix/inferior.scm				\
  guix/describe.scm				\
  guix/quirks.scm				\
  guix/channels.scm				\
  guix/gnu-maintenance.scm			\
  guix/self.scm					\
  guix/substitutes.scm				\
  guix/upstream.scm				\
  guix/licenses.scm				\
  guix/lint.scm				\
  guix/glob.scm					\
  guix/git.scm					\
  guix/git-authenticate.scm			\
  guix/graph.scm				\
  guix/cache.scm				\
  guix/cve.scm					\
  guix/workers.scm				\
  guix/least-authority.scm			\
  guix/read-print.scm				\
  guix/ipfs.scm					\
  guix/platform.scm                             \
  guix/platforms/arm.scm                        \
  guix/platforms/avr.scm                        \
  guix/platforms/mips.scm                       \
  guix/platforms/or1k.scm                       \
  guix/platforms/powerpc.scm                    \
  guix/platforms/riscv.scm                      \
  guix/platforms/x86.scm                        \
  guix/platforms/xtensa.scm                     \
  guix/build-system.scm				\
  guix/build-system/agda.scm			\
  guix/build-system/android-ndk.scm		\
  guix/build-system/ant.scm			\
  guix/build-system/asdf.scm			\
  guix/build-system/cargo.scm			\
  guix/build-system/channel.scm		\
  guix/build-system/chicken.scm		\
  guix/build-system/clojure.scm		\
  guix/build-system/cmake.scm			\
  guix/build-system/copy.scm			\
  guix/build-system/composer.scm		\
  guix/build-system/dub.scm			\
  guix/build-system/dune.scm			\
  guix/build-system/elm.scm			\
  guix/build-system/emacs.scm			\
  guix/build-system/font.scm			\
  guix/build-system/glib-or-gtk.scm		\
  guix/build-system/gnu.scm			\
  guix/build-system/go.scm			\
  guix/build-system/guile.scm			\
  guix/build-system/haskell.scm		\
  guix/build-system/julia.scm			\
  guix/build-system/linux-module.scm		\
  guix/build-system/maven.scm			\
  guix/build-system/meson.scm			\
  guix/build-system/minetest.scm		\
  guix/build-system/minify.scm			\
  guix/build-system/mix.scm			\
  guix/build-system/mozilla.scm		\
  guix/build-system/node.scm			\
  guix/build-system/ocaml.scm			\
  guix/build-system/perl.scm			\
  guix/build-system/pyproject.scm		\
  guix/build-system/python.scm			\
  guix/build-system/qt.scm			\
  guix/build-system/r.scm			\
  guix/build-system/rakudo.scm			\
  guix/build-system/rebar.scm			\
  guix/build-system/renpy.scm			\
  guix/build-system/ruby.scm			\
  guix/build-system/scons.scm			\
  guix/build-system/texlive.scm		\
  guix/build-system/tree-sitter.scm		\
  guix/build-system/trivial.scm		\
  guix/build-system/vim.scm			\
  guix/build-system/waf.scm			\
  guix/build-system/zig.scm			\
  guix/ftp-client.scm				\
  guix/http-client.scm				\
  guix/gnupg.scm				\
  guix/elf.scm					\
  guix/profiling.scm				\
  guix/store.scm				\
  guix/cvs-download.scm				\
  guix/svn-download.scm				\
  guix/colors.scm				\
  guix/i18n.scm					\
  guix/diagnostics.scm				\
  guix/ui.scm					\
  guix/status.scm				\
  guix/build/agda-build-system.scm              \
  guix/build/android-ndk-build-system.scm	\
  guix/build/ant-build-system.scm		\
  guix/build/download.scm			\
  guix/build/download-nar.scm			\
  guix/build/cargo-build-system.scm		\
  guix/build/cargo-utils.scm			\
  guix/build/chicken-build-system.scm		\
  guix/build/cmake-build-system.scm		\
  guix/build/composer-build-system.scm		\
  guix/build/dub-build-system.scm		\
  guix/build/dune-build-system.scm		\
  guix/build/elm-build-system.scm		\
  guix/build/emacs-build-system.scm		\
  guix/build/meson-build-system.scm		\
  guix/build/minify-build-system.scm		\
  guix/build/font-build-system.scm		\
  guix/build/go-build-system.scm		\
  guix/build/android-repo.scm			\
  guix/build/asdf-build-system.scm		\
  guix/build/bzr.scm				\
  guix/build/copy-build-system.scm		\
  guix/build/git.scm				\
  guix/build/hg.scm				\
  guix/build/glib-or-gtk-build-system.scm	\
  guix/build/gnu-bootstrap.scm			\
  guix/build/gnu-build-system.scm		\
  guix/build/gnu-dist.scm			\
  guix/build/guile-build-system.scm		\
  guix/build/maven-build-system.scm		\
  guix/build/minetest-build-system.scm		\
  guix/build/mix-build-system.scm		\
  guix/build/node-build-system.scm		\
  guix/build/perl-build-system.scm		\
  guix/build/pyproject-build-system.scm		\
  guix/build/python-build-system.scm		\
  guix/build/ocaml-build-system.scm		\
  guix/build/qt-build-system.scm		\
  guix/build/r-build-system.scm			\
  guix/build/renpy-build-system.scm			\
  guix/build/rakudo-build-system.scm		\
  guix/build/rebar-build-system.scm		\
  guix/build/ruby-build-system.scm		\
  guix/build/scons-build-system.scm		\
  guix/build/texlive-build-system.scm		\
  guix/build/tree-sitter-build-system.scm	\
  guix/build/vim-build-system.scm		\
  guix/build/waf-build-system.scm		\
  guix/build/haskell-build-system.scm		\
  guix/build/julia-build-system.scm		\
  guix/build/kconfig.scm			\
  guix/build/linux-module-build-system.scm	\
  guix/build/store-copy.scm			\
  guix/build/json.scm				\
  guix/build/pack.scm				\
  guix/build/utils.scm				\
  guix/build/union.scm				\
  guix/build/profiles.scm			\
  guix/build/compile.scm			\
  guix/build/cvs.scm				\
  guix/build/svn.scm				\
  guix/build/syscalls.scm                       \
  guix/build/gremlin.scm			\
  guix/build/debug-link.scm			\
  guix/build/clojure-build-system.scm		\
  guix/build/clojure-utils.scm			\
  guix/build/emacs-utils.scm			\
  guix/build/java-utils.scm			\
  guix/build/lisp-utils.scm			\
  guix/build/meson-configuration.scm		\
  guix/build/maven/java.scm			\
  guix/build/maven/plugin.scm			\
  guix/build/maven/pom.scm			\
  guix/build/graft.scm				\
  guix/build/bournish.scm			\
  guix/build/qt-utils.scm			\
  guix/build/zig-build-system.scm		\
  guix/build/make-bootstrap.scm			\
  guix/search-paths.scm				\
  guix/packages.scm				\
  guix/import/cabal.scm				\
  guix/import/composer.scm			\
  guix/import/cpan.scm				\
  guix/import/cran.scm				\
  guix/import/crate.scm				\
  guix/import/egg.scm   			\
  guix/import/elm.scm				\
  guix/import/elpa.scm   			\
  guix/import/gem.scm				\
  guix/import/git.scm                           \
  guix/import/github.scm   			\
  guix/import/gnome.scm				\
  guix/import/gnu.scm				\
  guix/import/go.scm				\
  guix/import/hackage.scm			\
  guix/import/hexpm.scm				\
  guix/import/json.scm				\
  guix/import/kde.scm				\
  guix/import/launchpad.scm   			\
  guix/import/minetest.scm   			\
  guix/import/npm-binary.scm			\
  guix/import/opam.scm				\
  guix/import/print.scm				\
  guix/import/pypi.scm				\
  guix/import/stackage.scm			\
  guix/import/test.scm   			\
  guix/import/texlive.scm   			\
  guix/import/utils.scm				\
  guix/scripts.scm				\
  guix/scripts/download.scm			\
  guix/scripts/perform-download.scm		\
  guix/scripts/build.scm			\
  guix/scripts/archive.scm			\
  guix/scripts/import.scm			\
  guix/scripts/package.scm			\
  guix/scripts/locate.scm			\
  guix/scripts/install.scm			\
  guix/scripts/remove.scm			\
  guix/scripts/upgrade.scm			\
  guix/scripts/search.scm			\
  guix/scripts/show.scm				\
  guix/scripts/gc.scm				\
  guix/scripts/hash.scm				\
  guix/scripts/pack.scm				\
  guix/scripts/pull.scm				\
  guix/scripts/processes.scm			\
  guix/scripts/substitute.scm			\
  guix/scripts/authenticate.scm			\
  guix/scripts/refresh.scm			\
  guix/scripts/repl.scm				\
  guix/scripts/describe.scm			\
  guix/scripts/style.scm			\
  guix/scripts/system.scm			\
  guix/scripts/system/edit.scm			\
  guix/scripts/system/reconfigure.scm		\
  guix/scripts/system/search.scm		\
  guix/scripts/home.scm			\
  guix/scripts/home/edit.scm			\
  guix/scripts/home/import.scm			\
  guix/scripts/lint.scm				\
  guix/scripts/challenge.scm			\
  guix/scripts/import/composer.scm		\
  guix/scripts/import/crate.scm			\
  guix/scripts/import/cpan.scm			\
  guix/scripts/import/cran.scm			\
  guix/scripts/import/egg.scm   		\
  guix/scripts/import/elm.scm			\
  guix/scripts/import/elpa.scm  		\
  guix/scripts/import/gem.scm			\
  guix/scripts/import/gnu.scm			\
  guix/scripts/import/go.scm			\
  guix/scripts/import/hackage.scm		\
  guix/scripts/import/hexpm.scm			\
  guix/scripts/import/json.scm  		\
  guix/scripts/import/minetest.scm  		\
  guix/scripts/import/npm-binary.scm		\
  guix/scripts/import/opam.scm			\
  guix/scripts/import/pypi.scm			\
  guix/scripts/import/stackage.scm		\
  guix/scripts/import/texlive.scm  		\
  guix/scripts/environment.scm			\
  guix/scripts/shell.scm			\
  guix/scripts/publish.scm			\
  guix/scripts/edit.scm				\
  guix/scripts/size.scm				\
  guix/scripts/git.scm				\
  guix/scripts/git/authenticate.scm		\
  guix/scripts/graph.scm			\
  guix/scripts/weather.scm			\
  guix/scripts/container.scm			\
  guix/scripts/container/exec.scm		\
  guix/scripts/deploy.scm			\
  guix/scripts/time-machine.scm			\
  guix.scm					\
  $(GNU_SYSTEM_MODULES)

if HAVE_GUILE_SSH

MODULES +=					\
  guix/ssh.scm					\
  guix/remote.scm				\
  guix/scripts/copy.scm				\
  guix/store/ssh.scm

endif HAVE_GUILE_SSH

if HAVE_GUILE_AVAHI

MODULES += 					\
  guix/avahi.scm				\
  guix/scripts/discover.scm

endif HAVE_GUILE_AVAHI

if BUILD_DAEMON_OFFLOAD

MODULES +=					\
  guix/scripts/offload.scm

endif BUILD_DAEMON_OFFLOAD

# Scheme implementation of the build daemon and related functionality.
STORE_MODULES =					\
  guix/store/database.scm			\
  guix/store/deduplication.scm			\
  guix/store/roots.scm

MODULES += $(STORE_MODULES)

# Internal modules with test suite support.
dist_noinst_DATA =				\
  guix/tests.scm				\
  guix/tests/http.scm				\
  guix/tests/git.scm				\
  guix/tests/gnupg.scm

# Auxiliary files for packages.
AUX_FILES =						\
  gnu/packages/aux-files/chromium/master-preferences.json		\
  gnu/packages/aux-files/emacs/comp-integrity.el		\
  gnu/packages/aux-files/emacs/comp-integrity-next.el		\
  gnu/packages/aux-files/emacs/guix-emacs.el		\
  gnu/packages/aux-files/findclass.php			\
  gnu/packages/aux-files/guix.vim			\
  gnu/packages/aux-files/linux-libre/6.10-arm.conf	\
  gnu/packages/aux-files/linux-libre/6.10-arm64.conf	\
  gnu/packages/aux-files/linux-libre/6.10-i686.conf	\
  gnu/packages/aux-files/linux-libre/6.10-x86_64.conf	\
  gnu/packages/aux-files/linux-libre/6.10-riscv.conf	\
  gnu/packages/aux-files/linux-libre/6.6-arm.conf	\
  gnu/packages/aux-files/linux-libre/6.6-arm64.conf	\
  gnu/packages/aux-files/linux-libre/6.6-i686.conf	\
  gnu/packages/aux-files/linux-libre/6.6-x86_64.conf	\
  gnu/packages/aux-files/linux-libre/6.1-arm.conf	\
  gnu/packages/aux-files/linux-libre/6.1-arm64.conf	\
  gnu/packages/aux-files/linux-libre/6.1-i686.conf	\
  gnu/packages/aux-files/linux-libre/6.1-x86_64.conf	\
  gnu/packages/aux-files/linux-libre/5.15-arm.conf	\
  gnu/packages/aux-files/linux-libre/5.15-arm64.conf	\
  gnu/packages/aux-files/linux-libre/5.15-i686.conf	\
  gnu/packages/aux-files/linux-libre/5.15-x86_64.conf	\
  gnu/packages/aux-files/linux-libre/5.10-arm.conf	\
  gnu/packages/aux-files/linux-libre/5.10-arm64.conf	\
  gnu/packages/aux-files/linux-libre/5.10-i686.conf	\
  gnu/packages/aux-files/linux-libre/5.10-x86_64.conf	\
  gnu/packages/aux-files/linux-libre/5.4-arm.conf	\
  gnu/packages/aux-files/linux-libre/5.4-arm64.conf	\
  gnu/packages/aux-files/linux-libre/5.4-i686.conf	\
  gnu/packages/aux-files/linux-libre/5.4-x86_64.conf	\
  gnu/packages/aux-files/linux-libre/4.19-arm.conf	\
  gnu/packages/aux-files/linux-libre/4.19-arm64.conf	\
  gnu/packages/aux-files/linux-libre/4.19-i686.conf	\
  gnu/packages/aux-files/linux-libre/4.19-x86_64.conf	\
  gnu/packages/aux-files/pack-audit.c			\
  gnu/packages/aux-files/python/sanity-check.py		\
  gnu/packages/aux-files/python/sitecustomize.py	\
  gnu/packages/aux-files/renpy/renpy.in	\
  gnu/packages/aux-files/run-in-namespace.c		\
  gnu/packages/aux-files/xml/patch-catalog-xml.xsl	\
  gnu/packages/aux-files/xml/docbook-xml/catalog-4.1.2.xml

# Templates, examples.
EXAMPLES =					\
  gnu/system/examples/asus-c201.tmpl		\
  gnu/system/examples/bare-bones.tmpl		\
  gnu/system/examples/bare-hurd.tmpl		\
  gnu/system/examples/beaglebone-black.tmpl	\
  gnu/system/examples/desktop.tmpl		\
  gnu/system/examples/lightweight-desktop.tmpl	\
  gnu/system/examples/docker-image.tmpl		\
  gnu/system/examples/plasma.tmpl		\
  gnu/system/examples/raspberry-pi-64.tmpl	\
  gnu/system/examples/raspberry-pi-64-nfs-root.tmpl	\
  gnu/system/examples/vm-image.tmpl

GOBJECTS = $(MODULES:%.scm=%.go) guix/config.go $(dist_noinst_DATA:%.scm=%.go)

nobase_dist_guilemodule_DATA =					\
  guix/d3.v3.js							\
  guix/graph.js							\
  guix/store/schema.sql						\
  $(MODULES) $(MODULES_NOT_COMPILED) $(AUX_FILES) $(EXAMPLES)	\
  $(MISC_DISTRO_FILES)
nobase_nodist_guilemodule_DATA = guix/config.scm
nobase_nodist_guileobject_DATA = $(GOBJECTS)

# Handy way to remove the .go files without removing all the rest.
clean-go:
	-$(RM) -f $(GOBJECTS)
	@find . -path ./test-tmp -prune -o -name '*.go' -print | \
	  if test -t 1; then \
	    xargs -r echo -e "\033[31mwarning:\033[0m stray .go files:"; \
	  else \
	    xargs -r echo "warning: stray .go files:"; \
	  fi


# Test extensions; has to be unconditional.
TEST_EXTENSIONS = .scm .sh

if CAN_RUN_TESTS

SCM_TESTS =					\
  tests/accounts.scm				\
  tests/base16.scm				\
  tests/base32.scm				\
  tests/base64.scm				\
  tests/boot-parameters.scm			\
  tests/bournish.scm				\
  tests/builders.scm				\
  tests/build-emacs-utils.scm			\
  tests/build-utils.scm			\
  tests/cache.scm				\
  tests/challenge.scm				\
  tests/channels.scm				\
  tests/combinators.scm			\
  tests/composer.scm				\
  tests/containers.scm				\
  tests/cpan.scm				\
  tests/cpio.scm				\
  tests/cran.scm				\
  tests/crate.scm				\
  tests/cve.scm				\
  tests/debug-link.scm				\
  tests/derivations.scm			\
  tests/discovery.scm				\
  tests/egg.scm				\
  tests/elm.scm				\
  tests/elpa.scm				\
  tests/file-systems.scm			\
  tests/gem.scm				\
  tests/gexp.scm				\
  tests/git.scm					\
  tests/git-authenticate.scm			\
  tests/glob.scm				\
  tests/gnu-maintenance.scm			\
  tests/grafts.scm				\
  tests/graph.scm				\
  tests/gremlin.scm				\
  tests/hackage.scm				\
  tests/home-import.scm				\
  tests/home-services.scm			\
  tests/http-client.scm				\
  tests/import-git.scm				\
  tests/import-github.scm			\
  tests/import-utils.scm			\
  tests/inferior.scm				\
  tests/lint.scm				\
  tests/minetest.scm				\
  tests/modules.scm				\
  tests/monads.scm				\
  tests/nar.scm				\
  tests/npm-binary.scm				\
  tests/networking.scm				\
  tests/opam.scm				\
  tests/openpgp.scm				\
  tests/packages.scm				\
  tests/pack.scm				\
  tests/pki.scm				\
  tests/print.scm				\
  tests/processes.scm				\
  tests/profiles.scm				\
  tests/publish.scm				\
  tests/pypi.scm				\
  tests/read-print.scm				\
  tests/records.scm				\
  tests/rpm.scm					\
  tests/scripts.scm				\
  tests/search-paths.scm			\
  tests/services.scm				\
  tests/services/file-sharing.scm		\
  tests/services/configuration.scm		\
  tests/services/lightdm.scm			\
  tests/services/linux.scm			\
  tests/services/pam-mount.scm			\
  tests/services/telephony.scm			\
  tests/services/vpn.scm			\
  tests/sets.scm				\
  tests/size.scm				\
  tests/status.scm				\
  tests/store-database.scm			\
  tests/store-deduplication.scm		\
  tests/store-roots.scm			\
  tests/store.scm				\
  tests/substitute.scm				\
  tests/swh.scm				\
  tests/syscalls.scm				\
  tests/system.scm				\
  tests/style.scm				\
  tests/texlive.scm				\
  tests/transformations.scm			\
  tests/ui.scm					\
  tests/union.scm				\
  tests/upstream.scm				\
  tests/utils.scm				\
  tests/uuid.scm				\
  tests/workers.scm

if HAVE_GUILE_LIB
SCM_TESTS += tests/go.scm
else
EXTRA_DIST += tests/go.scm
endif

if BUILD_DAEMON_OFFLOAD
SCM_TESTS  += tests/offload.scm
else
EXTRA_DIST += tests/offload.scm
endif

SH_TESTS =					\
  tests/guix-build.sh				\
  tests/guix-build-branch.sh			\
  tests/guix-download.sh			\
  tests/guix-gc.sh				\
  tests/guix-git-authenticate.sh		\
  tests/guix-hash.sh				\
  tests/guix-locate.sh				\
  tests/guix-pack.sh				\
  tests/guix-pack-localstatedir.sh		\
  tests/guix-pack-relocatable.sh		\
  tests/guix-package.sh				\
  tests/guix-package-aliases.sh			\
  tests/guix-package-net.sh			\
  tests/guix-style.sh				\
  tests/guix-system.sh				\
  tests/guix-home.sh				\
  tests/guix-archive.sh				\
  tests/guix-authenticate.sh			\
  tests/guix-environment.sh			\
  tests/guix-environment-container.sh		\
  tests/guix-refresh.sh				\
  tests/guix-shell.sh				\
  tests/guix-shell-export-manifest.sh		\
  tests/guix-time-machine.sh			\
  tests/guix-graph.sh				\
  tests/guix-describe.sh			\
  tests/guix-repl.sh     			\
  tests/guix-lint.sh

TESTS = $(SCM_TESTS) $(SH_TESTS)

AM_TESTS_ENVIRONMENT = abs_top_srcdir="$(abs_top_srcdir)" GUILE_AUTO_COMPILE=0

SCM_LOG_DRIVER =				\
  $(top_builddir)/test-env --quiet-stderr	\
  $(GUILE) --no-auto-compile -e main		\
      $(top_srcdir)/build-aux/test-driver.scm

AM_SCM_LOG_DRIVER_FLAGS = --brief=yes

SH_LOG_COMPILER = $(top_builddir)/test-env $(SHELL)
AM_SH_LOG_FLAGS = -x -e

# Make sure `tests/guix-gc.sh' runs last, after all the others.  Otherwise it
# could end up removing files from the store while they are being used by
# other instances of the daemon.
tests/guix-gc.log:							\
  $(patsubst %.sh,%.log,$(filter-out tests/guix-gc.sh,$(SH_TESTS)))	\
  $(SCM_TESTS:%.scm=%.log)

else !CAN_RUN_TESTS

TESTS =
SH_TESTS =
SCM_TESTS =

# Automake always generates a 'check' target, so better not override it.
check-local:
	@echo
	@echo "Cannot run tests because file name limits would be exceeded." >&2
	@echo "Look for 'length' in the 'config.log' file for details." >&2
	@echo
	@exit 1

endif !CAN_RUN_TESTS

check-system: $(GOBJECTS)
	$(AM_V_at)$(top_builddir)/pre-inst-env			\
	  guix build -m $(top_srcdir)/etc/system-tests.scm -K

# Public keys used to sign substitutes.
dist_pkgdata_DATA =				\
  etc/substitutes/berlin.guix.gnu.org.pub	\
  etc/substitutes/ci.guix.gnu.org.pub		\
  etc/substitutes/ci.guix.info.pub		\
  etc/substitutes/bordeaux.guix.gnu.org.pub

# Bash completion file.
dist_bashcompletion_DATA = etc/completion/bash/guix	\
  etc/completion/bash/guix-daemon

# Zsh completion file.
dist_zshcompletion_DATA = etc/completion/zsh/_guix

# Fish completion file.
dist_fishcompletion_DATA = etc/completion/fish/guix.fish

# SELinux policy
nodist_selinux_policy_DATA = etc/guix-daemon.cil

EXTRA_DIST +=						\
  .dir-locals.el					\
  .guix-authorizations					\
  .guix-channel						\
  CODE-OF-CONDUCT					\
  HACKING						\
  ROADMAP						\
  TODO							\
  bootstrap						\
  manifest.scm						\
  build-aux/build-self.scm				\
  build-aux/check-channel-news.scm			\
  build-aux/check-final-inputs-self-contained.scm	\
  build-aux/compile-all.scm				\
  build-aux/compile-as-derivation.scm			\
  build-aux/config.rpath				\
  build-aux/convert-xref.scm				\
  build-aux/generate-authors.scm			\
  build-aux/git-version-gen				\
  build-aux/mdate-from-git.scm				\
  build-aux/test-driver.scm				\
  build-aux/update-NEWS.scm				\
  build-aux/update-guix-package.scm			\
  build-aux/xgettext.scm				\
  doc/build.scm						\
  etc/disarchive-manifest.scm				\
  etc/guix-install.sh					\
  etc/historical-authorizations				\
  etc/news.scm						\
  etc/hurd-manifest.scm					\
  etc/kernels-manifest.scm				\
  etc/release-manifest.scm				\
  etc/source-manifest.scm				\
  etc/system-tests.scm					\
  etc/time-travel-manifest.scm				\
  scripts/guix.in					\
  tests/cve-sample.json					\
  tests/keys/civodul.pub				\
  tests/keys/dsa.pub					\
  tests/keys/ed25519-2.pub				\
  tests/keys/ed25519-2.sec				\
  tests/keys/ed25519-3.pub				\
  tests/keys/ed25519-3.sec				\
  tests/keys/ed25519.pub				\
  tests/keys/ed25519.sec				\
  tests/keys/rsa.pub					\
  tests/keys/signing-key.pub				\
  tests/keys/signing-key.sec				\
  tests/test.drv					\
  $(TESTS)

if !BUILD_DAEMON_OFFLOAD

EXTRA_DIST +=					\
  guix/scripts/offload.scm

endif !BUILD_DAEMON_OFFLOAD


CLEANFILES =					\
  $(bin_SCRIPTS)				\
  $(GOBJECTS)					\
  $(SCM_TESTS:tests/%.scm=%.log)

# Unset 'GUILE_LOAD_COMPILED_PATH' altogether while compiling.  Otherwise, if
# $GUILE_LOAD_COMPILED_PATH contains $(moduledir), we may find .go files in
# there that are newer than the local .scm files (for instance because the
# user ran 'make install' recently).  When that happens, we end up loading
# those previously-installed .go files, which may be stale, thereby breaking
# the whole thing.  Likewise, set 'XDG_CACHE_HOME' to avoid loading possibly
# stale files from ~/.cache/guile/ccache.
%.go: make-go ; @:
make-go: make-core-go make-packages-go make-system-go make-cli-go

# Define a rule to build a subset of the .go files.
define guile-compilation-rule

$(1): $(2)
	$(AM_V_at)echo "Compiling Scheme modules..." ;		\
	unset GUILE_LOAD_COMPILED_PATH ;			\
	XDG_CACHE_HOME=/nowhere					\
	host=$(host) srcdir="$(top_srcdir)"			\
	$(top_builddir)/pre-inst-env				\
	$(GUILE) -L "$(top_builddir)" -L "$(top_srcdir)"	\
	  --no-auto-compile					\
	  -s "$(top_srcdir)"/build-aux/compile-all.scm		\
	  --total $(words $(MODULES))				\
	  --completed $(3)					\
	  $$(filter %.scm,$$^)

endef

# Split compilation in several steps, each of which building a subset of
# $(MODULES).  The main goal is to reduce peak memory consumption, as reported
# in <https://issues.guix.gnu.org/48963>.  Each 'eval' call below creates a
# 'make-*-go' phony target that builds the corresponding subset.

first_fifth :=								\
  gnu/packages/a% gnu/packages/b% gnu/packages/c%

second_fifth :=								\
  gnu/packages/d% gnu/packages/e% gnu/packages/f%

third_fifth :=								\
  gnu/packages/g%  gnu/packages/h% gnu/packages/i%

fourth_fifth :=								\
  gnu/packages/j% gnu/packages/k% gnu/packages/l% gnu/packages/m% 	\
  gnu/packages/n% gnu/packages/o%

MODULES_CORE      := guix.scm $(filter-out guix/scripts/%,$(filter guix/%,$(MODULES)))
MODULES_PACKAGES1 := $(filter $(first_fifth),$(MODULES))
MODULES_PACKAGES2 := $(filter $(second_fifth),$(MODULES))
MODULES_PACKAGES3 := $(filter $(third_fifth),$(MODULES))
MODULES_PACKAGES4 := $(filter $(fourth_fifth),$(MODULES))
MODULES_PACKAGES5 := $(filter-out $(first_fifth) $(second_fifth)	\
			$(third_fifth) $(fourth_fifth),			\
			$(filter gnu/packages/%,$(MODULES)))
MODULES_PACKAGES  := $(MODULES_PACKAGES1) $(MODULES_PACKAGES2)		\
			$(MODULES_PACKAGES3) $(MODULES_PACKAGES4)	\
			$(MODULES_PACKAGES5)
MODULES_SYSTEM    := gnu.scm $(filter-out gnu/packages/%,$(filter gnu/%,$(MODULES)))
MODULES_CLI       := $(filter guix/scripts/%,$(MODULES))
MODULES_PO        := guix/build/po.scm

$(eval $(call guile-compilation-rule,make-core-go,	\
  $(MODULES_CORE) guix/config.scm $(dist_noinst_DATA),	\
  0))
.PHONY: make-core-go

$(eval $(call guile-compilation-rule,make-packages1-go,	\
  $(MODULES_PACKAGES1) make-core-go,			\
  $(words $(MODULES_CORE))))
.PHONY: make-packages1-go

$(eval $(call guile-compilation-rule,make-packages2-go,	\
  $(MODULES_PACKAGES2) make-core-go make-packages1-go,	\
  $(words $(MODULES_CORE) $(MODULES_PACKAGES1))))
.PHONY: make-packages2-go

$(eval $(call guile-compilation-rule,make-packages3-go,				\
  $(MODULES_PACKAGES3) make-core-go make-packages1-go make-packages2-go,	\
  $(words $(MODULES_CORE) $(MODULES_PACKAGES1) $(MODULES_PACKAGES2))))
.PHONY: make-packages3-go

$(eval $(call guile-compilation-rule,make-packages4-go,			\
  $(MODULES_PACKAGES4) make-core-go make-packages1-go make-packages2-go	\
    make-packages3-go,							\
  $(words $(MODULES_CORE) $(MODULES_PACKAGES1) $(MODULES_PACKAGES2)	\
    $(MODULES_PACKAGES3))))
.PHONY: make-packages4-go

$(eval $(call guile-compilation-rule,make-packages5-go,			\
  $(MODULES_PACKAGES5) make-core-go make-packages1-go make-packages2-go	\
    make-packages3-go make-packages4-go,				\
  $(words $(MODULES_CORE) $(MODULES_PACKAGES1) $(MODULES_PACKAGES2)	\
    $(MODULES_PACKAGES3) $(MODULES_PACKAGES4))))
.PHONY: make-packages5-go

make-packages-go: make-packages1-go make-packages2-go \
  make-packages3-go make-packages4-go make-packages5-go
.PHONY: make-packages-go

$(eval $(call guile-compilation-rule,make-system-go,	\
  $(MODULES_SYSTEM) make-packages-go make-core-go,	\
  $(words $(MODULES_CORE) $(MODULES_PACKAGES))))
.PHONY: make-system-go

$(eval $(call guile-compilation-rule,make-cli-go,			\
  $(MODULES_CLI) make-system-go make-packages-go make-core-go,		\
  $(words $(MODULES_CORE) $(MODULES_PACKAGES) $(MODULES_SYSTEM))))
.PHONY: make-cli-go

$(eval $(call guile-compilation-rule,guix/build/po.go,			\
  $(MODULES_PO),							\
  0))

SUFFIXES = .go

# Make sure source files are installed first, so that the mtime of
# installed compiled files is greater than that of installed source
# files.  See
# <http://lists.gnu.org/archive/html/guile-devel/2010-07/msg00125.html>
# for details.
guix_install_go_files = install-nobase_nodist_guileobjectDATA
$(guix_install_go_files): install-nobase_dist_guilemoduleDATA

# The above trick doesn't work for 'config.go' because both 'config.scm' and
# 'config.go' are listed in $(nobase_nodist_guileobject_DATA).  Thus, give it
# special treatment.
install-data-hook:
	touch "$(DESTDIR)$(guileobjectdir)/guix/config.go"

# Assuming Guix is already installed and the daemon is up and running, this
# rule builds from $(srcdir), creating and building derivations.
as-derivation:
	$(AM_V_at)echo "Building Guix in Guix..." ;		\
	$(GUILE) --no-auto-compile				\
	  "$(top_srcdir)/build-aux/compile-as-derivation.scm"	\
	  "$(abs_top_srcdir)"

SUBDIRS = po/guix po/packages
BUILT_SOURCES =

include doc/local.mk

if BUILD_DAEMON

include nix/local.mk

endif BUILD_DAEMON

ACLOCAL_AMFLAGS = -I m4

# Pass an explicit '--localstatedir' so that configure does not error out if
# it finds an existing installation with a different localstatedir.  Inherit
# 'ac_cv_guix_test_root' so that "make check" in $(distdir) does not have to
# repopulate the whole store, and to make sure $(GUIX_TEST_ROOT) is short
# enough for shebangs.
AM_DISTCHECK_CONFIGURE_FLAGS =			\
  --localstatedir="$$dc_install_base/var"	\
  --with-libgcrypt-prefix="$(LIBGCRYPT_PREFIX)"	\
  --with-libgcrypt-libdir="$(LIBGCRYPT_LIBDIR)"	\
  --enable-daemon				\
  ac_cv_guix_test_root="$(GUIX_TEST_ROOT)"

# The self-contained tarball.
guix-binary.%.tar.xz:
	$(AM_V_GEN)GUIX_PACKAGE_PATH=					\
	tarball=`$(top_builddir)/pre-inst-env guix pack -C xz		\
	  --fallback							\
	  -s "$*" --localstatedir --profile-name=current-guix		\
	  guix` ;					\
	cp "$$tarball" "$@.tmp" ; mv "$@.tmp" "$@"

# The `dist' target has other dependencies when building from Git
# to assert and achieve reproducibility.
if in_git_p

# The dependency on dist-doc-pot-update is to clean possibly stale doc and po
# files and only then generate the .pot files, which are not checked in.
dist: dist-doc-pot-update
dist-doc-pot-update: auto-clean
	$(MAKE) guile$(EXEEXT)
	$(MAKE) -C po/guix all
	$(MAKE) -C po/packages all
	$(MAKE) doc-pot-update

dist-hook: gen-ChangeLog gen-AUTHORS

# Assert that Autotools cache is up to date with Git, by checking
# PACKAGE_VERSION against HEAD.  Indented to get past Automake.
 ifeq ($(MAKECMDGOALS),dist)
 git_version = $(shell build-aux/git-version-gen .tarball-version)
 ifneq ($(PACKAGE_VERSION),$(git_version))
 $(warning Autotools cache out of date.)
 $(info Autotools cache version: $(PACKAGE_VERSION).)
 $(info Git version: $(git_version).)
 $(info Please run ./bootstrap && ./configure $(DIST_CONFIGURE_FLAGS))
 ifneq ($(GUIX_ALLOW_IRREPRODUCIBLE_TARBALL),yes)
 $(error Cannot create reproducible tarball)
 else
 $(warning Tarball will be irreproducible; distdir will not get removed!)
 endif # !GUIX_ALLOW_IRREPRODUCIBLE_TARBALL
 endif # PACKAGE_VERSION != git_version
 endif # MAKECMDGOALS dist

else # !in_git_p

dist: doc-pot-update

 ifeq ($(MAKECMDGOALS),dist)
$(warning Not using Git, tarball will likely be irreproducible!)
 endif # MAKECMDGOALS dist
endif # !in_git_p

dist-hook: gen-tarball-version
dist-hook: assert-no-store-file-names

distcheck-hook: assert-binaries-available assert-final-inputs-self-contained

EXTRA_DIST += $(top_srcdir)/.version
BUILT_SOURCES += $(top_srcdir)/.version
$(top_srcdir)/.version: config.status
	$(AM_V_GEN)echo $(VERSION) > "$@-t" && mv "$@-t" "$@"

gen-tarball-version:
	echo $(VERSION) > "$(distdir)/.tarball-version"
	echo $(SOURCE_DATE_EPOCH) > $(distdir)/.tarball-timestamp

gen-ChangeLog:
	$(AM_V_GEN)if test -d $(top_srcdir)/.git; then		\
	  set -e;						\
	  export LC_ALL=en_US.UTF-8;				\
	  export TZ=UTC0;					\
	  $(top_srcdir)/build-aux/gitlog-to-changelog		\
	    > $(distdir)/ChangeLog.tmp;				\
	  rm -f $(distdir)/ChangeLog;				\
	  mv $(distdir)/ChangeLog.tmp $(distdir)/ChangeLog;	\
	fi

gen-AUTHORS:
	$(AM_V_GEN)if test -d $(top_srcdir)/.git; then		\
	  set -e;						\
	  rm -f "$(distdir)/AUTHORS";				\
	  export LC_ALL=en_US.UTF-8;				\
	  export TZ=UTC0;					\
	  $(top_builddir)/pre-inst-env "$(GUILE)"		\
	    "$(top_srcdir)/build-aux/generate-authors.scm"	\
	    "$(top_srcdir)" "$(distdir)/AUTHORS";

# Like 'dist', but regenerate 'configure' so we get an up-to-date
# 'PACKAGE_VERSION' string.  (In Gnulib, 'GNUmakefile' has a special trick to
# do that whenever a 'dist' target is used.)
dist-with-updated-version:
	@echo "Running './bootstrap' for new version string..."
	$(top_srcdir)/bootstrap
	$(MAKE) $(AM_MAKEFLAGS) $(top_srcdir)/.version dist

.PHONY: dist-with-updated-version


#
# Release management.
#

# Reproducible tarball
override GZIP_ENV = --best --no-name
# Be friendly to Debian; avoid using EPOCH
override am__tar = $${TAR-tar}			\
 --format=ustar					\
 --sort=name					\
 --mode=go=rX,u+rw,a-s				\
 --mtime=@$$(cat "$$tardir"/.tarball-timestamp)	\
 --owner=0 --group=0 --numeric-owner		\
 -cf -						\
 "$$tardir"

releasedir = release-$(PACKAGE_VERSION)

PACKAGE_FULL_TARNAME = $(PACKAGE_TARNAME)-$(PACKAGE_VERSION)

# List of source tarballs produced.  This must be kept in sync with the
# 'dist-' options of 'AM_INIT_AUTOMAKE' in 'configure.ac'.
SOURCE_TARBALLS =					\
  $(foreach ext,tar.gz,$(PACKAGE_FULL_TARNAME).$(ext))

# Systems supported by Guix.
SUPPORTED_SYSTEMS ?= x86_64-linux i686-linux armhf-linux aarch64-linux \
  powerpc64le-linux

# Guix binary tarballs.
BINARY_TARBALLS =							\
  $(foreach system,$(SUPPORTED_SYSTEMS),guix-binary.$(system).tar.xz)

# Systems supported by Guix System.
GUIX_SYSTEM_SUPPORTED_SYSTEMS ?= x86_64-linux i686-linux

# Systems for which we build Guix VMs.
GUIX_SYSTEM_VM_SYSTEMS ?= x86_64-linux

# Prefix of the Guix installation image file name.
GUIX_SYSTEM_IMAGE_BASE = guix-system-install-$(PACKAGE_VERSION)

# Prefix of the Guix VM image file name.
GUIX_SYSTEM_VM_IMAGE_BASE = guix-system-vm-image-$(PACKAGE_VERSION)

# Flags for 'guix system vm-image'.  By default create a VM image that appears
# to have a 20G hard disk.
GUIX_SYSTEM_VM_IMAGE_FLAGS ?= --image-size=30G

# Return the sequence of '-s' flags for the given systems.
system_flags = $(foreach system,$(1),-s $(system))

# The release process works in several phases:
#
#   0. We assume the developer created a 'vX.Y.Z' tag.
#   1. Build the source tarball.
#   2. Update the 'guix' package so that it corresponds to the 'vX.Y.Z' tag.
#   3. Build the binary tarballs for that 'guix' package.
#   4. Update the 'guix' package again.
#   5. Build the installation and VM images.  The images will run 'guix'
#      corresponding to 'vX.Y.Z' + 1 commit, and they will install 'vX.Y.Z'.
#
# This 'release' target takes care of everything and copies the resulting
# files to $(releasedir).
#
# XXX: Depend on 'dist' rather than 'distcheck' to work around the Gettext
# issue described at <https://savannah.gnu.org/bugs/index.php?51027>.
release: dist-with-updated-version all
	@if ! git diff-index --quiet HEAD; then			\
	  echo "There are uncommitted changes; stopping." >&2 ;	\
	  exit 1 ;						\
	fi
	$(MKDIR_P) "$(releasedir)"
	rm -f "$(releasedir)"/*
	mv $(SOURCE_TARBALLS) "$(releasedir)"
# Bump the Guix package version and build it.
	GUIX_ALLOW_ME_TO_USE_PRIVATE_COMMIT=yes \
	$(top_builddir)/pre-inst-env "$(GUILE)"	\
		$(top_srcdir)/build-aux/update-guix-package.scm	\
	   	"`git rev-parse HEAD`" "$(PACKAGE_VERSION)"
	git add $(top_srcdir)/gnu/packages/package-management.scm
	git commit -m "gnu: guix: Update to $(PACKAGE_VERSION)."
	$(top_builddir)/pre-inst-env guix build guix	\
	      $(call system_flags,$(SUPPORTED_SYSTEMS))	\
	      -v1 --no-grafts --fallback
# Generate the binary release tarballs.
	rm -f $(BINARY_TARBALLS)
	$(MAKE) $(BINARY_TARBALLS)
	for system in $(SUPPORTED_SYSTEMS) ; do					\
	  mv "guix-binary.$$system.tar.xz"					\
	      "$(releasedir)/guix-binary-$(PACKAGE_VERSION).$$system.tar.xz" ;	\
	done
# Build 'current-guix' to speed things up for the next step.
	$(top_builddir)/pre-inst-env guix build				\
	      -e '((@ (gnu packages package-management) current-guix))'	\
	      $(call system_flags,$(GUIX_SYSTEM_SUPPORTED_SYSTEMS))	\
	      -v1 --no-grafts --fallback
# Generate the ISO installation images.
	for system in $(GUIX_SYSTEM_SUPPORTED_SYSTEMS) ; do				\
	  GUIX_DISPLAYED_VERSION="`git describe --match=v* | sed -'es/^v//'`" ;		\
	  image=`$(top_builddir)/pre-inst-env						\
	    guix system image -t iso9660						\
	    --label="GUIX_$${system}_$(VERSION)"					\
            --system=$$system --fallback						\
	    gnu/system/install.scm` ;							\
	  if [ ! -f "$$image" ] ; then							\
	    echo "failed to produce Guix installation image for $$system" >&2 ;		\
	    exit 1 ;									\
	  fi ;										\
	  cp "$$image" "$(releasedir)/$(GUIX_SYSTEM_IMAGE_BASE).$$system.iso.tmp" ;	\
	  mv "$(releasedir)/$(GUIX_SYSTEM_IMAGE_BASE).$$system.iso.tmp"			\
	     "$(releasedir)/$(GUIX_SYSTEM_IMAGE_BASE).$$system.iso" ;			\
	done
# Generate the VM images.
	for system in $(GUIX_SYSTEM_VM_SYSTEMS) ; do					\
	  GUIX_DISPLAYED_VERSION="`git describe --match=v* | sed -'es/^v//'`" ;		\
	  image=`$(top_builddir)/pre-inst-env						\
	    guix system image -t qcow2 $(GUIX_SYSTEM_VM_IMAGE_FLAGS)			\
	    --save-provenance								\
	    --system=$$system --fallback						\
	    gnu/system/examples/vm-image.tmpl` ;					\
	  if [ ! -f "$$image" ] ; then							\
	    echo "failed to produce Guix VM image for $$system" >&2 ;			\
	    exit 1 ;									\
	  fi ;										\
	  cp "$$image" "$(releasedir)/$(GUIX_SYSTEM_VM_IMAGE_BASE).$$system.qcow2";	\
	done
	@echo
	@echo "Congratulations!  All the release files are now in $(releasedir)."
	@echo

update-guix-package:
	git rev-parse HEAD
	$(top_builddir)/pre-inst-env "$(GUILE)"			\
	   $(top_srcdir)/build-aux/update-guix-package.scm	\
	   "`git rev-parse HEAD`"

# Location of a checkout of <git://git.savannah.gnu.org/guix/maintenance.git>.
# Package data from this checkout is used by 'update-NEWS.scm'.
GUIX_MAINTENANCE_DIRECTORY ?= $(top_srcdir)/../guix-maintenance

update-NEWS: $(GOBJECTS)
	$(top_builddir)/pre-inst-env "$(GUILE)"				\
	  $(top_srcdir)/build-aux/update-NEWS.scm			\
	  $(top_srcdir)/NEWS "$(GUIX_MAINTENANCE_DIRECTORY)/data"

# Make sure we're not shipping a file that embeds a local /gnu/store file name.
assert-no-store-file-names:
	$(AM_V_at)if grep -r --exclude=*.texi --exclude=*.info			\
	     --exclude=*.info-[0-9] --exclude=*.dot				\
	     --exclude=*.eps --exclude-dir=bootstrap				\
	     --exclude=guix-manual.pot --exclude=guix-manual.*.po		\
	     --exclude=guix-cookbook.pot --exclude=guix-cookbook.*.po		\
	     --exclude=guix-prettify.el						\
	     --exclude=ChangeLog*						\
	     --exclude=binutils-boot-2.20*.patch				\
	     -E "$(storedir)/[a-z0-9]{32}-" $(distdir) ;			\
	then									\
	  echo "error: store file names embedded in the distribution" >&2 ;	\
	  exit 1 ;								\
	fi

# Make sure important substitutes are available.  Check only the primary
# server so that '--display-missing' doesn't print two lists.
assert-binaries-available: $(GOBJECTS)
	$(AM_V_at)$(top_builddir)/pre-inst-env				\
	  guix weather -m "$(top_srcdir)/etc/release-manifest.scm"	\
	                --substitute-urls="https://ci.guix.gnu.org"	\
	                --display-missing

# Make sure the final inputs don't refer to bootstrap tools.
assert-final-inputs-self-contained: $(GOBJECTS)
	$(AM_V_at)$(top_builddir)/pre-inst-env "$(GUILE)"			\
	  "$(top_srcdir)/build-aux/check-final-inputs-self-contained.scm"

# Validate channel news.
check-channel-news: $(GOBJECTS)
	$(AM_V_at)$(top_builddir)/pre-inst-env "$(GUILE)"	\
	  "$(top_srcdir)/build-aux/check-channel-news.scm"

# Compute the Cuirass jobs.
cuirass-jobs: $(GOBJECTS)
	rm -rf "$@"
	$(AM_V_at)$(MKDIR_P) "$@"
	$(AM_V_GEN)$(top_builddir)/pre-inst-env "$(GUILE)"		\
	  "$(top_srcdir)/build-aux/cuirass/evaluate.scm" "$@"

.PHONY: gen-ChangeLog gen-AUTHORS gen-tarball-version
.PHONY: assert-no-store-file-names assert-binaries-available
.PHONY: assert-final-inputs-self-contained check-channel-news
.PHONY: clean-go make-go as-derivation
.PHONY: update-guix-package update-NEWS cuirass-jobs release

# Git auto-configuration.
.git/hooks/%: etc/git/%
	$(AM_V_at)if test -d .git; then \
	cp "$<" "$@"; \
	fi

.git/config: etc/git/gitconfig
	$(AM_V_at)if command -v git >/dev/null && test -d .git; then \
	git config --fixed-value --replace-all include.path \
	  ../etc/git/gitconfig ../etc/git/gitconfig; \
	fi

COMMIT_MSG_MAGIC = VGhpcyBpcyB0aGUgY29tbWl0LW1zZyBob29rIG9mIEd1aXg=
.git/hooks/commit-msg: etc/git/commit-msg
	$(AM_V_at)if test -d .git; then \
	if test -f $@  && ! grep -qF $(COMMIT_MSG_MAGIC) $@; then \
	  mkdir -p $@.d && mv $@ $@.d && \
	@ echo user commit-msg hook moved to $@.d/commit-msg; \
	fi; \
	cp etc/git/commit-msg $@; \
	fi

# The etc/git/ config files are not distributed and have no use when building
# from a tarball.  Do not add dependencies on these to *_DATA when building
# from a tarball, as that breaks the build.
if in_git_p
nodist_noinst_DATA =				\
  .git/hooks/pre-push				\
  .git/hooks/post-merge				\
  .git/config					\
  .git/hooks/commit-msg
endif

# Downloading up-to-date PO files.

WEBLATE_REPO = https://framagit.org/tyreunom/guix-translations

# Shallow clone the Git repository behind Weblate and copy files from it if
# they contain at least one translation, and they are well-formed (Scheme
# format only), warn otherwise.  Copied files are converted to a canonical
# form.
download-po:
	dir=$$(mktemp -d); \
	git clone --depth 1 "$(WEBLATE_REPO)" "$$dir/translations" && \
	for domain in po/doc po/guix po/packages; do \
	    for po in "$$dir/translations/$$domain"/*.po; do \
	        translated=$$(LANG=en_US.UTF-8 msgfmt --statistics "$$po" 2>&1 | cut -f1 -d' '); \
	        untranslated=$$(LANG=en_US.UTF-8 msgfmt --statistics "$$po" 2>&1 | rev | cut -f3 -d' ' | rev); \
	        untranslated=$${untranslated:-0}; \
	        total=$$(($$translated+$$untranslated)); \
	        target=$$(basename "$$po"); \
	        target="$$domain/$$target"; \
	        msgfmt -c "$$po"; \
	        if msgfmt -c "$$po" && [ "$$translated" != "0" ] && ([ "$$domain" != "po/doc" ] || [ "$$translated" -gt $$(($$total/10)) ] || [ -f $$target ]); then \
	            msgfilter --no-wrap -i "$$po" cat > "$$po".tmp; \
	            mv "$$po".tmp "$$target"; \
	            echo "copied $$target."; \
	        else \
	            echo "WARN: $$target ($$translated translated messages ($$((translated/total*100))%)) was not added/updated."; \
	        fi; \
	    done; \
	done; \
	for po in po/doc/*.po; do \
	    translated=$$(LANG=en_US.UTF-8 msgfmt --statistics "$$po" 2>&1 | cut -f1 -d' '); \
	    untranslated=$$(LANG=en_US.UTF-8 msgfmt --statistics "$$po" 2>&1 | rev | cut -f3 -d' ' | rev); \
	    untranslated=$${untranslated:-0}; \
	    total=$$(($$translated + $$untranslated)); \
	    if [ "$$translated" -lt "$$(($$total/20))" ]; then \
	        echo "WARN: $$po was removed because it is below the 5% threshold: $$((translated/total*100))%"; \
	        rm $$po; \
	    fi; \
	done; \
	rm -rf "$$dir"
.PHONY: download-po

## -------------- ##
## Silent rules.  ##
## -------------- ##

AM_V_DL = $(AM_V_DL_$(V))
AM_V_DL_ = $(AM_V_DL_$(AM_DEFAULT_VERBOSITY))
AM_V_DL_0 = @echo "  DL      " $@;

AM_V_DOT = $(AM_V_DOT_$(V))
AM_V_DOT_ = $(AM_V_DOT_$(AM_DEFAULT_VERBOSITY))
AM_V_DOT_0 = @echo "  DOT     " $@;

AM_V_HELP2MAN = $(AM_V_HELP2MAN_$(V))
AM_V_HELP2MAN_ = $(AM_V_HELP2MAN_$(AM_DEFAULT_VERBOSITY))
AM_V_HELP2MAN_0 = @echo "  HELP2MAN" $@;

AM_V_PO4A = $(AM_V_PO4A_$(V))
AM_V_PO4A_ = $(AM_V_PO4A_$(AM_DEFAULT_VERBOSITY))
AM_V_PO4A_0 = @echo "  PO4A    " $@;

AM_V_POXREF = $(AM_V_POXREF_$(V))
AM_V_POXREF_ = $(AM_V_POXREF_$(AM_DEFAULT_VERBOSITY))
AM_V_POXREF_0 = @echo "  POXREF  " $@;
generated by cgit
s;annotation)) (sha256 (base32 "0lp94r9dsx8sl1ifysavgjf4aamhjc4n71zif5jyfnwmzpj7g4ml")))) (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) (build-system r-build-system) (propagated-inputs (list r-bsgenome r-genomeinfodb)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") (synopsis "Full genome sequences for Homo sapiens") (description "This package provides full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") (license license:artistic2.0))) (define-public r-ensdb-hsapiens-v75 (package (name "r-ensdb-hsapiens-v75") (version "2.99.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) (sha256 (base32 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) (properties `((upstream-name . "EnsDb.Hsapiens.v75"))) (build-system r-build-system) (propagated-inputs (list r-ensembldb)) (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") (synopsis "Ensembl based annotation package") (description "This package exposes an annotation database generated from Ensembl.") (license license:artistic2.0))) (define-public r-ensdb-hsapiens-v86 (package (name "r-ensdb-hsapiens-v86") (version "2.99.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnsDb.Hsapiens.v86" version 'annotation)) (sha256 (base32 "1gp7xrzddpvmh2vrcp571wyy00skxgxfl39ksj4h0hm1qay0fb2m")))) (properties `((upstream-name . "EnsDb.Hsapiens.v86"))) (build-system r-build-system) (propagated-inputs (list r-ensembldb)) (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v86") (synopsis "Ensembl based annotation package") (description "This package exposes an annotation database generated from Ensembl.") (license license:artistic2.0))) (define-public r-ensdb-mmusculus-v79 (package (name "r-ensdb-mmusculus-v79") (version "2.99.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnsDb.Mmusculus.v79" version 'annotation)) (sha256 (base32 "1zpmq7v55if6q9r0h883q9k8l70ym20b01m9hxf121wb256rl9f7")))) (properties `((upstream-name . "EnsDb.Mmusculus.v79"))) (build-system r-build-system) (propagated-inputs (list r-ensembldb)) (home-page "https://bioconductor.org/packages/EnsDb.Mmusculus.v79") (synopsis "Ensembl based annotation package") (description "This package exposes an annotation database generated from Ensembl.") (license license:artistic2.0))) (define-public r-escape (package (name "r-escape") (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "escape" version)) (sha256 (base32 "03wbrxd7kjyl3d4s418ql5fv7bmwdfyfp10jd8knr0xis7vxmz2x")))) (properties `((upstream-name . "escape"))) (build-system r-build-system) (propagated-inputs (list r-aucell r-biocparallel r-dplyr r-ggdist r-ggplot2 r-ggpointdensity r-ggridges r-gseabase r-gsva r-matrixgenerics r-msigdbr r-patchwork r-reshape2 r-seuratobject r-singlecellexperiment r-stringr r-summarizedexperiment r-ucell)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/escape") (synopsis "Single cell analysis platform for enrichment") (description "R-escape streamlines gene set enrichment analysis for single-cell RNA sequencing. Using raw count information, Seurat objects, or @code{SingleCellExperiment} format, users can perform and visualize GSEA across individual cells.") (license license:gpl2))) (define-public r-snplocs-hsapiens-dbsnp144-grch37 (package (name "r-snplocs-hsapiens-dbsnp144-grch37") (version "0.99.20") (source (origin (method url-fetch) (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" version 'annotation)) (sha256 (base32 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) (build-system r-build-system) ;; As this package provides little more than a very large data file it ;; doesn't make sense to build substitutes. (arguments `(#:substitutable? #f)) (propagated-inputs (list r-biocgenerics r-s4vectors r-iranges r-genomeinfodb r-genomicranges r-bsgenome r-biostrings)) (home-page "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") (description "This package provides SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).") (license license:artistic2.0))) (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene (package (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene") (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene" version 'annotation)) (sha256 (base32 "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4")))) (properties `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene") (synopsis "Annotation package for TxDb object(s)") (description "This package exposes an annotation databases generated from UCSC by exposing these as TxDb objects.") (license license:artistic2.0))) (define-public r-txdb-hsapiens-ucsc-hg19-knowngene (package (name "r-txdb-hsapiens-ucsc-hg19-knowngene") (version "3.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene" version 'annotation)) (sha256 (base32 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) (properties `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) (build-system r-build-system) (propagated-inputs (list r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") (synopsis "Annotation package for human genome in TxDb format") (description "This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" track. The database is exposed as a @code{TxDb} object.") (license license:artistic2.0))) (define-public r-txdb-hsapiens-ucsc-hg38-knowngene (package (name "r-txdb-hsapiens-ucsc-hg38-knowngene") (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" version 'annotation)) (sha256 (base32 "0ak6acjll2djamakpn60ks47lfs2y0r8xwhjazj6fvch34xkc2d5")))) (properties `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") (synopsis "Annotation package for human genome in TxDb format") (description "This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" track. The database is exposed as a @code{TxDb} object.") (license license:artistic2.0))) (define-public r-txdb-mmusculus-ucsc-mm9-knowngene (package (name "r-txdb-mmusculus-ucsc-mm9-knowngene") (version "3.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene" version 'annotation)) (sha256 (base32 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) (build-system r-build-system) (propagated-inputs (list r-genomicfeatures r-annotationdbi)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") (synopsis "Annotation package for mouse genome in TxDb format") (description "This package provides an annotation database of Mouse genome data. It is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The database is exposed as a @code{TxDb} object.") (license license:artistic2.0))) (define-public r-txdb-mmusculus-ucsc-mm10-knowngene (package (name "r-txdb-mmusculus-ucsc-mm10-knowngene") (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene" version 'annotation)) (sha256 (base32 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9")))) (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) (propagated-inputs (list r-bsgenome r-genomicfeatures r-annotationdbi)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") (description "This package loads a TxDb object, which is an R interface to prefabricated databases contained in this package. This package provides the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) based on the knownGene track.") (license license:artistic2.0))) (define-public r-txdb-celegans-ucsc-ce6-ensgene (package (name "r-txdb-celegans-ucsc-ce6-ensgene") (version "3.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene" version 'annotation)) (sha256 (base32 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90")))) (properties `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") (synopsis "Annotation package for C elegans TxDb objects") (description "This package exposes a C elegans annotation database generated from UCSC by exposing these as TxDb objects.") (license license:artistic2.0))) (define-public r-fdb-infiniummethylation-hg19 (package (name "r-fdb-infiniummethylation-hg19") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19" version 'annotation)) (sha256 (base32 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) (properties `((upstream-name . "FDb.InfiniumMethylation.hg19"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") (description "This is an annotation package for Illumina Infinium DNA methylation probes. It contains the compiled HumanMethylation27 and HumanMethylation450 annotations.") (license license:artistic2.0))) (define-public r-illuminahumanmethylationepicmanifest (package (name "r-illuminahumanmethylationepicmanifest") (version "0.3.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest" version 'annotation)) (sha256 (base32 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) (properties `((upstream-name . 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It also contains a collection of 12 datasets to use with @code{MethylClock} package to estimate chronological and gestational DNA methylation with estimators to use with different methylation clocks.") (license license:expat))) (define-public r-mousegastrulationdata (package (name "r-mousegastrulationdata") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MouseGastrulationData" version 'experiment)) (sha256 (base32 "0adw98vym1jir1jrzaws7zrlfvls6rfl8bvkpq5sjy4crb33lxy2")))) (properties `((upstream-name . 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"minfiData"))) (build-system r-build-system) (propagated-inputs (list r-illuminahumanmethylation450kanno-ilmn12-hg19 r-illuminahumanmethylation450kmanifest r-minfi)) (home-page "https://bioconductor.org/packages/minfiData") (synopsis "Example data for the Illumina Methylation 450k array") (description "This package provides data from 6 samples across 2 groups from 450k methylation arrays.") (license license:artistic2.0))) (define-public r-msdata (package (name "r-msdata") (version "0.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msdata" version 'experiment)) (sha256 (base32 "0g7mlgks3nfnfipnybs7pvsnmrvmq8888g39badca8pi73q1cm25")))) (properties `((upstream-name . "msdata"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/msdata") (synopsis "Various Mass Spectrometry raw data example files") (description "This package provides Ion Trap positive ionization mode data in mzML file format. It includes a subset from 500-850 m/z and 1190-1310 seconds, including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5; LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example files for various search engines.") (license license:gpl2+))) (define-public r-msexperiment (package (name "r-msexperiment") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsExperiment" version)) (sha256 (base32 "0dxv3jw5aj1i73vqrp3c031pj26i7rp0q2zs4nq3x1vni349506d")))) (properties `((upstream-name . 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To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.") (license license:artistic2.0))) (define-public r-msigdb (package (name "r-msigdb") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msigdb" version 'experiment)) (sha256 (base32 "080wm9sjwqhaxqx1r3kly1bi1gvkssqpsadnvabx11w493356qr0")))) (properties `((upstream-name . "msigdb"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-annotationhub r-experimenthub r-gseabase r-org-hs-eg-db r-org-mm-eg-db)) (native-inputs (list r-knitr)) (home-page "https://doi.org/doi:10.18129/B9.bioc.msigdb") (synopsis "ExperimentHub package for the molecular signatures database") (description "R-msigdb provides the Molecular Signatures Database in a R accessible objects. Signatures are stored in @code{GeneSet} class objects form the GSEABase package and the entire database is stored in a @code{GeneSetCollection} object. These data are then hosted on the @code{ExperimentHub}. Data used in this package was obtained from the @code{MSigDB} of the Broad Institute. Metadata for each gene set is stored along with the gene set in the @code{GeneSet} class object.") (license license:cc-by4.0))) (define-public r-pasilla (package (name "r-pasilla") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pasilla" version 'experiment)) (sha256 (base32 "0r5i64125qq5z4c8zliazsi68035d1bsz6ingzqdh37m8prdw1cr")))) (build-system r-build-system) (propagated-inputs (list r-dexseq)) (native-inputs (list r-knitr)) (home-page "https://www.bioconductor.org/packages/pasilla/") (synopsis "Data package with per-exon and per-gene read counts") (description "This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article 'Conservation of an RNA regulatory map between Drosophila and mammals' by Brooks et al., Genome Research 2011.") 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Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.") (license license:artistic2.0))) (define-public r-all (package (name "r-all") (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALL" version 'experiment)) (sha256 (base32 "1yl8b8q8i19kx4viwinhyq9xn9d4axlfgjvm7cpf7pys4krhnrha")))) (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/ALL") (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") (description "The data consist of microarrays from 128 different individuals with @dfn{acute lymphoblastic leukemia} (ALL). 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(license license:gpl2+))) ;;; Packages (define-public r-abarray (package (name "r-abarray") (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABarray" version)) (sha256 (base32 "1kfqq4df55pxl7gnwf24aaryxijym4gzqfjyif28arlbjci9hlv6")))) (properties `((upstream-name . "ABarray"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest)) (home-page "https://bioconductor.org/packages/ABarray") (synopsis "Gene expression analysis for Applied Biosystems Genome Survey Microarray") (description "The package @code{ABarray} is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be transformed into expression data matrix. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A @dfn{graphical user interface} (GUI) is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.") (license license:gpl2+))) (define-public r-absseq (package (name "r-absseq") (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 "0zqb2w055x4whgl3mljarsnps6lkz90fwlx2lnirbnrgmlnalwjz")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) (home-page "https://bioconductor.org/packages/ABSSeq") (synopsis "RNA-Seq analysis based on modelling absolute expression differences") (description "This package implements a new RNA-Seq analysis method and integrates two modules: a basic model for pairwise comparison and a linear model for complex design. RNA-Seq quantifies gene expression with reads count, which usually consists of conditions (or treatments) and several replicates for each condition. This software infers differential expression directly by the counts difference between conditions. It assumes that the sum counts difference between conditions follow a negative binomial distribution. In addition, @code{ABSSeq} moderates the fold-changes by two steps: the expression level and gene-specific dispersion, that might facilitate the gene ranking by fold-change and visualization.") (license license:gpl3+))) (define-public r-adacgh2 (package (name "r-adacgh2") (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADaCGH2" version)) (sha256 (base32 "1j9dn0xw8mdfvi2ccm1d5j9q740wb89wqi6715n6jy3dljlc8irz")))) (properties `((upstream-name . 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(license license:gpl3+))) (define-public r-adam (package (name "r-adam") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 "0z0rmpwfhd8p6c4zscviwsningsm740r3pb95cl8brasfdg1kl3v")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-dt r-go-db r-keggrest r-knitr r-pbapply r-rcpp r-stringr r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/ADAM") (synopsis "Gene activity and diversity analysis module") (description "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA) package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions. 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The @code{ADImpute} package proposes two methods to address this issue: @enumerate @item a gene regulatory network-based approach using gene-gene relationships learnt from external data; @item a baseline approach corresponding to a sample-wide average. @end enumerate @code{ADImpute} implements these novel methods and also combines them with existing imputation methods like @code{DrImpute} and @code{SAVER}. @code{ADImpute} can learn the best performing method per gene and combine the results from different methods into an ensemble.") (license license:gpl3+))) (define-public r-adsplit (package (name "r-adsplit") (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 "13rrkb0vxkknvqhb8pgx8d13sxzy3w0wbkhhj5lrlc1kb1yqcfbh")))) (properties `((upstream-name . 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It provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. It includes @code{GRanges} generation and plotting functions.") ;; GPLv3 with additional liability disclaimer. (license license:gpl3))) (define-public r-drimseq (package (name "r-drimseq") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 (base32 "10skx3n3r9vp1p1499ddccgabi7q3cy1dpi5pbp4ap0gff5ika5x")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biocparallel r-edger r-genomicranges r-ggplot2 r-iranges r-limma r-mass r-reshape2 r-s4vectors)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DRIMSeq") (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq") (description "The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.") (license license:gpl3+))) (define-public r-dropletutils (package (name "r-dropletutils") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DropletUtils" version)) (sha256 (base32 "01y88cnii02sn1jgyvvmbx8j60qbzqyznqfxzv06yi4y0xj37klg")))) (properties `((upstream-name . 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(define-public r-dsb (package (name "r-dsb") (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "dsb" version)) (sha256 (base32 "16y0l3nmg88ihsr03f5n151jirypf7pxy6q0cgx2vpmdnqynlh61")))) (properties `((upstream-name . "dsb"))) (build-system r-build-system) (propagated-inputs (list r-limma r-magrittr r-mclust)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/niaid/dsb") (synopsis "Normalize & denoise droplet single cell protein data (CITE-Seq)") (description "R-dsb improves protein expression analysis in droplet-based single-cell studies. The package specifically addresses noise in raw protein UMI counts from methods like CITE-seq. It identifies and removes two main sources of noise—protein-specific noise from unbound antibodies and droplet/cell-specific noise. The package is applicable to various methods, including CITE-seq, REAP-seq, ASAP-seq, TEA-seq, and Mission Bioplatform data. Check the vignette for tutorials on integrating dsb with Seurat and Bioconductor, and using dsb in Python.") (license license:cc0))) (define-public r-dss (package (name "r-dss") (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DSS" version)) (sha256 (base32 "1y9xg6ic3a03xswyfvyxdhnd7ngkljc96bm5fry4ni6kpa77bkv8")))) (properties `((upstream-name . "DSS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-bsseq)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DSS") (synopsis "Dispersion shrinkage for sequencing data") (description "DSS is an R library performing differential analysis for count-based sequencing data. It detects @dfn{differentially expressed genes} (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from @dfn{bisulfite sequencing} (BS-seq). The core of DSS is a dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-dyndoc (package (name "r-dyndoc") (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DynDoc" version)) (sha256 (base32 "174jfdyq7g7mvn7wvmdkf36n0n969aqsg9bwd1nk6a5nw1khm7js")))) (properties `((upstream-name . "DynDoc"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/DynDoc") (synopsis "Dynamic document tools") (description "This package provides a set of functions to create and interact with dynamic documents and vignettes.") 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(define-public r-isva (package (name "r-isva") (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "isva" version)) (sha256 (base32 "05qx9q0kg4ma23v4abhihw0vz017nq6hv2jzsiqx4d20ngh1dl4z")))) (properties `((upstream-name . "isva"))) (build-system r-build-system) (propagated-inputs (list r-fastica r-jade r-qvalue)) (home-page "https://cran.r-project.org/package=isva") (synopsis "Independent surrogate variable analysis") (description "Independent Surrogate Variable Analysis is an algorithm for feature selection in the presence of potential confounding factors (see Teschendorff AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).") (license license:gpl2))) (define-public r-italics (package (name "r-italics") (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ITALICS" version)) (sha256 (base32 "06h6iqrqzlcj4hyhj1ikl9isr3ls1pph49v5n7cp87czinr0nd3s")))) (properties `((upstream-name . 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(define-public r-absfiltergsea (package (name "r-absfiltergsea") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "AbsFilterGSEA" version)) (sha256 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) (properties `((upstream-name . "AbsFilterGSEA"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") (synopsis "Improved false positive control of gene-permuting with absolute filtering") (description "This package provides a function that performs gene-permuting of a gene-set enrichment analysis (GSEA) calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.") (license license:gpl2))) ;; This is a CRAN package, but it depends on r-biobase from Bioconductor. (define-public r-bisquerna (package (name "r-bisquerna") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "BisqueRNA" version)) (sha256 (base32 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n")))) (properties `((upstream-name . "BisqueRNA"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-limsolve)) (native-inputs (list 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 abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples.") (license license:gpl3))) ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 ;; from Bioconductor. (define-public r-deconstructsigs (package (name "r-deconstructsigs") (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "deconstructSigs" version)) (sha256 (base32 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) (properties `((upstream-name . "deconstructSigs"))) (build-system r-build-system) (propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb r-reshape2)) (home-page "https://github.com/raerose01/deconstructSigs") (synopsis "Identifies signatures present in a tumor sample") (description "This package takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on Bioconductor packages. (define-public r-jetset (package (name "r-jetset") (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "jetset" version)) (sha256 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp")))) (properties `((upstream-name . "jetset"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-org-hs-eg-db)) (home-page "http://www.cbs.dtu.dk/biotools/jetset/") (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays") (description "This package provides a one-to-one mapping from gene to \"best\" probe set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a, hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single gene may be measured by multiple probe sets. This can present a mild conundrum when attempting to evaluate a gene \"signature\" that is defined by gene names rather than by specific probe sets. This package also includes the pre-calculated probe set quality scores that were used to define the mapping.") (license license:artistic2.0))) (define-public r-nebulosa (package (name "r-nebulosa") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Nebulosa" version)) (sha256 (base32 "0m5z6rribsrk9mzcksjh0nmpf4d0x0hn8jd80h0hj0hj8sj1ifgv")))) (properties `((upstream-name . "Nebulosa"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggrastr r-ks r-matrix r-patchwork r-seuratobject r-singlecellexperiment r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/powellgenomicslab/Nebulosa") (synopsis "Single-cell data visualisation using kernel gene-weighted density estimation") (description "This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). @code{Seurat} and @code{SingleCellExperiment} objects can be used within Nebulosa.") (license license:gpl3))) ;; This is a CRAN package but it requires r-rcy3, a Bioconductor package. (define-public r-netgsa (package (name "r-netgsa") (version "4.0.5") (source (origin (method url-fetch) (uri (cran-uri "netgsa" version)) (sha256 (base32 "1m9myxsbvbljr038azxzakpbh20a21qhiy20d0ipvjc5asq3kfla")))) (properties `((upstream-name . "netgsa"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-corpcor r-data-table r-dplyr r-genefilter r-glassofast r-glmnet r-graph r-graphite r-httr r-igraph r-magrittr r-matrix r-msigdbr r-org-hs-eg-db r-quadprog r-rcpp r-rcppeigen r-rcy3 r-reshape2 r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/mikehellstern/netgsa") (synopsis "Network-Based gene set analysis") (description "This package lets you carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. 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"NMF"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocmanager r-bigmemory ;suggested r-cluster r-codetools r-colorspace r-digest r-doparallel r-foreach r-ggplot2 r-gridbase r-rcolorbrewer r-registry r-reshape2 r-rngtools r-stringr r-synchronicity)) ;suggested (native-inputs (list r-knitr)) (home-page "https://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description "This package provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new or custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.") 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In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.") (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 (list r-biostrings r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-iranges r-seqlogo 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.") 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"muscat"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-blme r-complexheatmap r-data-table r-deseq2 r-dplyr r-edger r-ggplot2 r-glmmtmb r-limma r-lme4 r-lmertest r-matrix r-matrixstats r-progress r-purrr r-s4vectors r-scales r-scater r-sctransform r-scuttle r-singlecellexperiment r-summarizedexperiment r-variancepartition r-viridis)) (native-inputs (list r-knitr)) (home-page "https://github.com/HelenaLC/muscat") (synopsis "Multi-sample multi-group scRNA-seq data analysis tools") (description "This package @code{muscat} provides various methods and visualization tools for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.") (license license:gpl3))) (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 "0smf4l023ckwsm5ckrqqw7kjyi1awp378mzhab7v8nk9n5smsj61")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-biocgenerics r-biostrings r-bsgenome ;; These two packages are suggested packages r-bsgenome-hsapiens-1000genomes-hs37d5 r-bsgenome-hsapiens-ucsc-hg19 r-cowplot r-dplyr r-genomeinfodb r-genomicranges r-ggalluvial r-ggdendro r-ggplot2 r-iranges r-magrittr r-nmf r-pracma r-purrr r-rcolorbrewer r-s4vectors r-stringr r-tibble r-tidyr 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-msa (package (name "r-msa") (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "msa" version)) (sha256 (base32 "16ixhinhcbf2nvdmqria231s4qhr8lzhr7yqr7ljrnnwiqadfr67")))) (properties `((upstream-name . "msa"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biostrings r-iranges r-rcpp r-s4vectors)) (native-inputs (list r-knitr)) (home-page "http://www.bioinf.jku.at/software/msa/") (synopsis "Multiple sequence alignment") (description "The msa package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.") (license license:gpl2+))) (define-public r-msnbase (package (name "r-msnbase") (version "2.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 "0cdvi2mjvhj0h8x2rh3kkzrdnmzhr7d9a41m21r6b843a0q7hp6f")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-biocgenerics r-biocparallel r-digest r-ggplot2 r-impute r-iranges r-lattice r-maldiquant r-mass r-mscoreutils r-mzid r-mzr r-pcamethods r-plyr r-protgenerics r-psmatch r-rcpp r-s4vectors r-scales r-vsn)) (native-inputs (list 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 "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 "0misrm4x4z5h8dfwcrwi24nhcjslqvbyk5n7qz6kf2zcgcwq8q44")))) (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 (list r-annotationdbi r-annotationhub r-biobase r-biocgenerics r-biocstyle r-biostrings r-data-table r-doparallel r-dplyr r-foreach r-ggplot2 r-iterators r-msmstests r-msnbase r-mzid r-mzr r-protgenerics r-purrr r-r-cache r-rcpp r-reshape2 r-rlang r-runit r-stringr r-tibble 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 "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 "0kh9swzh3hvi6qi64cgr13f22s1mgvz2rid5psb1gy4l3biwadj5")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-iterators r-plyr r-protgenerics r-xml)) (native-inputs (list 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 "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 "02dz23xns9ryz98nip1w68h9q5ckxpyl1zvzklsp4j7p9z2400dk")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) (properties `((upstream-name . "mzR") (updater-extra-inputs . ("boost")))) (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")))))))) (inputs (list boost ; use this instead of the bundled boost sources zlib)) (propagated-inputs (list r-biobase r-biocgenerics r-ncdf4 r-protgenerics r-rcpp r-rhdf5lib)) (native-inputs (list 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))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-numbat (package (name "r-numbat") (version "1.3.2-1") (source (origin (method url-fetch) (uri (cran-uri "numbat" version)) (sha256 (base32 "1b9bykgw3z7a8bky5yv2g402gdapv8kcla2kbbyqvs77x4wba4q4")))) (properties `((upstream-name . "numbat"))) (build-system r-build-system) (propagated-inputs (list r-ape r-catools r-data-table r-dendextend r-dplyr r-genomicranges r-ggplot2 r-ggraph r-ggtree r-glue r-igraph r-iranges r-logger r-magrittr r-matrix r-optparse r-paralleldist r-patchwork r-pryr r-purrr r-r-utils r-rcpp r-rcpparmadillo r-rhpcblasctl r-roptim r-scales r-scistreer r-stringr r-tibble r-tidygraph r-tidyr r-vcfr r-zoo)) (home-page "https://github.com/kharchenkolab/numbat") (synopsis "Haplotype-aware CNV analysis from scRNA-Seq") (description "This package provides a computational method that infers copy number variations (CNV) in cancer scRNA-seq data and reconstructs the tumor phylogeny. It integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. It does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). It can be used to: @enumerate @item detect allele-specific copy number variations from single-cells @item differentiate tumor versus normal cells in the tumor microenvironment @item infer the clonal architecture and evolutionary history of profiled tumors @end enumerate For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y, Gao et al in Nature Biotechnology 2022}.") (license license:expat))) (define-public r-organism-dplyr (package (name "r-organism-dplyr") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 "03z5pyqbaxwyrq5m858c8k69fwvclq98ksr84dc4m7r8lzz2hfxx")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-annotationfilter r-biocfilecache r-dbi r-dbplyr r-dplyr r-genomeinfodb r-genomicfeatures r-genomicranges r-iranges r-rlang r-rsqlite r-s4vectors r-tibble)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Organism.dplyr") (synopsis "Dplyr-based access to Bioconductor annotation resources") (description "This package provides an alternative interface to Bioconductor @code{ annotation} resources, in particular the gene identifier mapping functionality of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate functionality of the @code{TxDb} packages (e.g., @code{TxDb.Hsapiens.UCSC.hg38.knownGene}).") (license license:artistic2.0))) (define-public r-organismdbi (package (name "r-organismdbi") (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 "1cfh632rpmklmyd5cibwiy0i2pk2kk2m39g8mq5sxfwd2am4r0jk")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biobase r-biocgenerics r-biocmanager r-dbi r-genomicfeatures r-genomicranges r-graph r-iranges r-rbgl r-s4vectors r-txdbmaker)) (native-inputs (list r-knitr)) (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-oscope (package (name "r-oscope") (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Oscope" version)) (sha256 (base32 "16d2ngakdg73rdx0bf1pz3z1n8npjzl3b7dn94g9zbayw4vp3x5z")))) (properties `((upstream-name . "Oscope"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) (home-page "https://bioconductor.org/packages/Oscope") (synopsis "Oscillatory genes identifier in unsynchronized single cell RNA-seq") (description "Oscope is a oscillatory genes identifier in unsynchronized single cell RNA-seq. This statistical pipeline has been developed to identify and recover the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.") (license license:asl2.0))) (define-public r-pcaexplorer (package (name "r-pcaexplorer") (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 "1szl2gyhw55ad4phcb7qn14amjb6xg65l3p4hnjzp6rda2cy9437")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-pcamethods (package (name "r-pcamethods") (version "1.96.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 "1hrq0xmpr1l95hyi6ls9r86ahwf2rcbvr8m7cpg6ra0gsfyn4mpi")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-mass 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-pfamanalyzer (package (name "r-pfamanalyzer") (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pfamAnalyzeR" version)) (sha256 (base32 "06bp5nghgrj8qyzqp1v869vck1j10093r9dp67w0kav4x4srkyyl")))) (properties `((upstream-name . "pfamAnalyzeR"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-readr r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/pfamAnalyzeR") (synopsis "Identification of domain isotypes in pfam data") (description "This R package enables the user to read pfam predictions into R. Most human protein domains exist as multiple distinct variants termed domain isotypes. This R package enables the identification and classification of such domain isotypes from pfam data.") (license license:expat))) (define-public r-piano (package (name "r-piano") (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "piano" version)) (sha256 (base32 "0v168wkwxzh70h2c08ad4dzlgklbgvx1fzwrzw2mqq0fyczj0diw")))) (properties `((upstream-name . "piano"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-dt r-fgsea r-gplots r-htmlwidgets r-igraph r-marray r-relations r-scales r-shiny r-shinydashboard r-shinyjs r-visnetwork)) (native-inputs (list r-knitr)) (home-page "https://varemo.github.io/piano/") (synopsis "Platform for integrative analysis of omics data") (description "Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The package contains functions for combining the results of multiple runs of gene set analyses.") (license license:gpl2+))) (define-public r-polyester (package (name "r-polyester") (version "1.39.0") (source (origin (method url-fetch) (uri (bioconductor-uri "polyester" version)) (sha256 (base32 "0fw0qhmbygjq4ryspyqikb8rxfn33ks000j7sshgfg8hf2rmqg3x")))) (properties `((upstream-name . "polyester"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-iranges r-limma r-logspline r-s4vectors r-zlibbioc)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/polyester") (synopsis "Simulate RNA-seq reads") (description "The polyester package simulates RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression.") (license license:artistic2.0))) (define-public r-powertcr (package (name "r-powertcr") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "powerTCR" version)) (sha256 (base32 "04w6jhpc1vkqrm3dr5igp1iwkammmi53mqafjz694n379hamxrhg")))) (properties `((upstream-name . "powerTCR"))) (build-system r-build-system) (propagated-inputs (list r-cubature r-doparallel r-evmix r-foreach r-magrittr r-purrr r-truncdist r-vegan r-vgam)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/powerTCR") (synopsis "Model-based comparative analysis of the TCR repertoire") (description "This package provides a model for the clone size distribution of the @acronym{TCR, T-cell receptor} repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on a Bioconductor package: ;; r-aroma-light, r-dnacopy.. (define-public r-pscbs (package (name "r-pscbs") (version "0.67.0") (source (origin (method url-fetch) (uri (cran-uri "PSCBS" version)) (sha256 (base32 "1gnd2nkh587dqpnbk5fsai7hx261vm405550rhlxffvs366x3596")))) (properties `((upstream-name . "PSCBS"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'install 'change-home-dir (lambda _ ;; Change from /homeless-shelter to /tmp for write permission. (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-aroma-light r-dnacopy r-future r-listenv r-matrixstats r-r-cache r-r-methodss3 r-r-oo r-r-utils)) (native-inputs (list r-r-rsp ;used to build vignettes r-r-devices)) (home-page "https://github.com/HenrikBengtsson/PSCBS") (synopsis "Analysis of parent-specific DNA copy numbers") (description "This is a package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (license license:gpl2+))) (define-public r-psmatch (package (name "r-psmatch") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PSMatch" version)) (sha256 (base32 "13w145is3d95392qqdq6qh3mrlcixbj0jzz4r590xas1qjp5d03h")))) (properties `((upstream-name . "PSMatch"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biocparallel r-igraph r-matrix r-mscoreutils r-protgenerics r-qfeatures r-s4vectors)) (native-inputs (list r-knitr)) (home-page "https://github.com/RforMassSpectrometry/PSM") (synopsis "Handling and managing peptide spectrum matches") (description "The PSMatch package helps proteomics practitioners to load, handle and manage peptide spectrum matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.") (license license:artistic2.0))) (define-public r-protgear (package (name "r-protgear") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "protGear" version)) (sha256 (base32 "1wbdp7f55lbn0gcxgnp9xk0y5npn7jmk9vp7yq9v76j7f396vj2f")))) (properties `((upstream-name . "protGear"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases ;; Needed by styler for writing to caches. (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-biobase r-data-table r-dplyr r-factoextra r-factominer r-flexdashboard r-genefilter r-ggally r-ggplot2 r-ggpubr r-gtools r-htmltools r-kendall r-knitr r-limma r-magrittr r-mass r-pheatmap r-plotly r-plyr r-purrr r-readr r-remotes r-rlang r-rmarkdown r-shiny r-shinydashboard r-styler r-tibble r-tidyr r-vsn)) (native-inputs (list r-knitr)) (home-page "https://github.com/Keniajin/protGear") (synopsis "Protein micro array data management and interactive visualization") (description "This package provides a generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance. These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.") (license license:gpl3))) (define-public r-protgenerics (package (name "r-protgenerics") (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 "0h0i4dgsgvyhma5pfvycv6wyxv27vp0b2i8b6l8hj55z8cvmvfln")))) (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-pwalign (package (name "r-pwalign") (version "1.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pwalign" version)) (sha256 (base32 "1m0j1m5jif5spd9fkpzz3z3c9s8vwiy8xvpx8rz8igxj89rwrwb7")))) (properties `((upstream-name . 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(define-public r-valr (package (name "r-valr") (version "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 "1pp8naglh26yi8c2p15arx8jkj3jyslzw7j3n5bnzngdpfprk3as")))) (build-system r-build-system) (propagated-inputs (list r-broom r-cli r-dplyr r-ggplot2 r-lifecycle r-rcpp r-readr r-rlang r-rtracklayer r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/rnabioco/valr") (synopsis "Genome interval arithmetic in R") (description "This package enables you to read and manipulate genome intervals and signals. It provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data.") 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This package supports the independent phyloseq data format and expands the available toolkit in order to facilitate the standardization of the analyses and the development of best practices.") (license license:bsd-2))) ;; This is a CRAN package but it depends on phyloseq, which is from ;; Bioconductor. (define-public r-microbiomestat (package (name "r-microbiomestat") (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "MicrobiomeStat" version)) (sha256 (base32 "1kpc68sl63k104xy7r6f3gxan0yx0rs7ksn8ldbq8xla00ddflgq")))) (properties `((upstream-name . 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"miloR"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biocneighbors r-biocparallel r-biocsingular r-cowplot r-dplyr r-edger r-ggbeeswarm r-ggplot2 r-ggraph r-ggrepel r-gtools r-igraph r-irlba r-limma r-matrix r-matrixgenerics r-matrixstats r-numderiv r-patchwork r-rcolorbrewer r-rcpp r-rcpparmadillo r-s4vectors r-singlecellexperiment r-stringr r-summarizedexperiment r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://marionilab.github.io/miloR") (synopsis "Differential neighbourhood abundance testing on a graph") (description "Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using a negative bionomial generalized linear model.") (license license:gpl3))) (define-public r-minfi (package (name "r-minfi") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 "1hk44wddcygh4j7jmj1b0p40hf5qdy1m78x14j19h7z9aq4azdij")))) (build-system r-build-system) (propagated-inputs (list r-beanplot r-biobase r-biocgenerics r-biocparallel r-biostrings r-bumphunter r-data-table r-delayedarray r-delayedmatrixstats r-genefilter r-genomeinfodb r-genomicranges r-geoquery r-hdf5array r-illuminaio r-iranges r-lattice r-limma r-mass r-mclust r-nlme r-nor1mix r-preprocesscore r-quadprog r-rcolorbrewer r-reshape r-s4vectors r-siggenes r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/hansenlab/minfi") (synopsis "Analyze Illumina Infinium DNA methylation arrays") (description "This package provides tools to analyze and visualize Illumina Infinium methylation arrays.") (license license:artistic2.0))) (define-public r-missmethyl (package (name "r-missmethyl") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "missMethyl" version)) (sha256 (base32 "0fnqa7v6lgld4pdqnvgdzly73aj4a4cn8sgszicxsyn1damxsjiw")))) (properties `((upstream-name . 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The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.") (license license:gpl2))) (define-public r-methylumi (package (name "r-methylumi") (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 "1ms3w43yvy810mr6dml9hqp3kw5jlpr9153kd62gvhjsgikaj3ja")))) (build-system r-build-system) (propagated-inputs (list r-annotate r-annotationdbi r-biobase r-biocgenerics r-fdb-infiniummethylation-hg19 r-genefilter r-genomeinfodb r-genomicfeatures r-genomicranges r-ggplot2 r-illuminaio r-iranges r-lattice r-matrixstats r-minfi r-reshape2 r-s4vectors r-scales r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/methylumi") (synopsis "Handle Illumina methylation data") (description "This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An \"intelligent\" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.") (license license:gpl2))) (define-public r-lefser (package (name "r-lefser") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lefser" version)) (sha256 (base32 "1qi4q3vijys4q1gfnflvvz8ws3j6f65rpprpgmrkqgiwfn7dvi6g")))) (properties `((upstream-name . "lefser"))) (build-system r-build-system) (propagated-inputs (list r-coin r-dplyr r-ggplot2 r-mass r-s4vectors r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/waldronlab/lefser") (synopsis "LEfSE method for microbiome biomarker discovery") (description "Lefser is an implementation in R of the popular \"LDA Effect Size\" (LEfSe) method for microbiome biomarker discovery. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers of groups and sub-groups.") (license license:artistic2.0))) (define-public r-lumi (package (name "r-lumi") (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 "04r7dw00yvjrxs0h6mwh79lwp55f5v8s4pgmzcy2fnpb2cdslpzy")))) (build-system r-build-system) (propagated-inputs (list r-affy r-annotate r-annotationdbi r-biobase r-dbi r-genomicfeatures r-genomicranges r-kernsmooth r-lattice r-mass r-methylumi r-mgcv r-nleqslv r-preprocesscore r-rsqlite)) (home-page "https://bioconductor.org/packages/lumi") (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") (description "The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.") (license license:lgpl2.0+))) (define-public r-linnorm (package (name "r-linnorm") (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 "1la6fwaap7957rrb4cs6w48kjz4hqrw3h39lpps419d4cbnsp5jz")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs (list r-amap r-apcluster r-ellipse r-fastcluster r-fpc r-ggdendro r-ggplot2 r-gmodels r-igraph r-limma r-mass r-mclust r-rcpp r-rcpparmadillo r-rtsne r-statmod r-vegan r-zoo)) (native-inputs (list r-knitr)) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large scale count data. It transforms such datasets for parametric tests. In addition to the transformtion function (@code{Linnorm}), the following pipelines are implemented: @enumerate @item Library size/batch effect normalization (@code{Linnorm.Norm}) @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means clustering or hierarchical clustering (@code{Linnorm.tSNE}, @code{Linnorm.PCA}, @code{Linnorm.HClust}) @item Differential expression analysis or differential peak detection using limma (@code{Linnorm.limma}) @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) @item Stable gene selection for scRNA-seq data; for users without or who do not want to rely on spike-in genes (@code{Linnorm.SGenes}) @item Data imputation (@code{Linnorm.DataImput}). @end enumerate Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the @code{RnaXSim} function is included for simulating RNA-seq data for the evaluation of DEG analysis methods.") (license license:expat))) (define-public r-ioniser (package (name "r-ioniser") (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 "1ihski4akl70v6kq03di6w1pz63dx6rxgmyjkm0dv0nhgkmrza22")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biocparallel r-biostrings r-bit64 r-dplyr r-ggplot2 r-magrittr r-rhdf5 r-shortread r-stringr r-tibble r-tidyr r-xvector)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description "IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.") (license license:expat))) ;; This is a CRAN package, but it depends on multtest from Bioconductor. (define-public r-mutoss (package (name "r-mutoss") (version "0.1-13") (source (origin (method url-fetch) (uri (cran-uri "mutoss" version)) (sha256 (base32 "0hgi9wpy3ai23dk6cdba6r118vvmgw210racsg3n1p24rv6ny3xn")))) (properties `((upstream-name . "mutoss"))) (build-system r-build-system) (propagated-inputs (list r-multcomp r-multtest r-mvtnorm r-plotrix)) (home-page "https://github.com/kornl/mutoss/") (synopsis "Unified multiple testing procedures") (description "This package is designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying mutossGUI package.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) ;; This is a CRAN package, but it depends on mutoss, which depends on multtest ;; from Bioconductor, so we put it here. (define-public r-metap (package (name "r-metap") (version "1.11") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 "1dwk402kbxigz5llh223z0b98cq2vs3ij049fgsj7bna7kycks1l")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mathjaxr r-mutoss r-qqconf r-rdpack r-tfisher)) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description "The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for meta-analysis of significance values including the methods of Edgington, 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 "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 "1kgvvvwvj3dgb2wik3y8j44ynda94bi05vvmiwlayrypqprwi1c1")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-edger r-ggplot2 r-igraph r-magrittr r-mass r-matrix r-matrixstats r-mgcv r-pbapply r-princurve r-rcolorbrewer r-s4vectors r-singlecellexperiment r-slingshot r-summarizedexperiment r-tibble r-trajectoryutils r-viridis)) (native-inputs (list 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") (version "1.29.0") (source (origin (method url-fetch) (uri (bioconductor-uri "triform" version)) (sha256 (base32 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-iranges r-yaml)) (home-page "https://bioconductor.org/packages/triform/") (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") (description "The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.") (license license:gpl2))) (define-public r-varianttools (package (name "r-varianttools") (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 "1idil9vkd5risx9ahkagdacnj2g2a11gzsd7wmhg5gjmr77r53ww")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel r-biostrings r-bsgenome r-genomeinfodb r-genomicfeatures r-genomicranges r-iranges r-matrix r-rsamtools r-rtracklayer r-s4vectors r-variantannotation)) (home-page "https://bioconductor.org/packages/VariantTools/") (synopsis "Tools for exploratory analysis of variant calls") (description "Explore, diagnose, and compare variant calls using filters. The VariantTools package supports a workflow for loading data, calling single sample variants and tumor-specific somatic mutations or other sample-specific variant types (e.g., RNA editing). Most of the functions operate on alignments (BAM files) or datasets of called variants. The user is expected to have already aligned the reads with a separate tool, e.g., GSNAP via gmapR.") (license license:artistic2.0))) (define-public r-heatplus (package (name "r-heatplus") (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 "1pc63hk0smcflq4903hvs4pp8r0kzlx08j0m1kxlh14cxwppamyb")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer)) (home-page "https://github.com/alexploner/Heatplus") (synopsis "Heatmaps with row and/or column covariates and colored clusters") (description "This package provides tools to display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.") (license license:gpl2+))) (define-public r-gosemsim (package (name "r-gosemsim") (version "2.30.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 "009rh51mndpkqw9vmr836ll2zsmsb4wlrjhvda5qiggznlhixrcv")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-dbi r-digest r-go-db r-httr2 r-r-utils r-rcpp r-rlang r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/GOSemSim") (synopsis "GO-terms semantic similarity measures") (description "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters.") (license license:artistic2.0))) (define-public r-anota (package (name "r-anota") (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 "1pg9p6982901k08iqpk0cdb9hii3k7bci9gq6an711r8a4iy3lmc")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) (home-page "https://bioconductor.org/packages/anota/") (synopsis "Analysis of translational activity") (description "Genome wide studies of translational control is emerging as a tool to study various biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e., differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallel the library performs a number of tests to assure that the data set is suitable for such analysis.") (license license:gpl3))) (define-public r-anota2seq (package (name "r-anota2seq") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota2seq" version)) (sha256 (base32 "140k37wswl4w2136pz9y0z82sphzxmgzgk3cr400kkm39wjn7vxm")))) (properties `((upstream-name . 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Analysis of translational efficiency aims to identify changes in translation efficiency leading to altered protein levels that are independent of total mRNA levels or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels.") (license license:gpl3))) (define-public r-fcscan (package (name "r-fcscan") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 (base32 "1gb15zrv44yn65wns7dk24rp54qv7wafqxgk1q8jnbkq9lp5wj2y")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-fgsea (package (name "r-fgsea") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 "0nnvqsyrj24h5y8qw8llk9f4jgy0v734k37kcksfcpja17frdyjy")))) (build-system r-build-system) (propagated-inputs (list r-bh r-biocparallel r-cowplot r-data-table r-fastmatch r-ggplot2 r-matrix r-rcpp r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/ctlab/fgsea/") (synopsis "Fast gene set enrichment analysis") (description "The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm makes more permutations and gets more fine grained p-values, which allows using accurate standard approaches to multiple hypothesis correction.") (license license:expat))) (define-public r-dose (package (name "r-dose") (version "3.30.4") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 "07pljijlyp4labxg4q3kf6wq4acw6axyyw57k1bws3hcf4m1d92x")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biocparallel r-fgsea r-ggplot2 r-gosemsim r-qvalue r-reshape2)) (native-inputs (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/DOSE/") (synopsis "Disease ontology semantic and enrichment analysis") (description "This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang, respectively, for measuring semantic similarities among @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.") (license license:artistic2.0))) (define-public r-enrichedheatmap (package (name "r-enrichedheatmap") (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnrichedHeatmap" version)) (sha256 (base32 "0fmqz9xqs1108a5xxpsc63pplcc0i742r4zdk46p68my28ba2xfq")))) (properties `((upstream-name . "EnrichedHeatmap"))) (build-system r-build-system) (propagated-inputs (list r-circlize r-complexheatmap r-genomicranges r-getoptlong r-iranges r-locfit r-matrixstats r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/EnrichedHeatmap") (synopsis "Enriched heatmaps") (description "Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. This type of heatmap is just a normal heatmap but with some special settings, with the functionality of @code{ComplexHeatmap}, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.") (license license:expat))) (define-public r-enrichplot (package (name "r-enrichplot") (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 "03p0a1vyaznk405xpkp57f22wg8x7lxiipjh101p7dq97rbzr4r7")))) (build-system r-build-system) (propagated-inputs (list r-aplot r-dose r-ggfun r-ggnewscale r-ggplot2 r-ggraph r-ggtree r-gosemsim r-igraph r-magrittr r-plyr r-purrr r-rcolorbrewer r-reshape2 r-rlang r-scatterpie r-shadowtext r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description "The enrichplot package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analyses. All the visualization methods are developed based on ggplot2 graphics.") 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(license license:artistic2.0))) (define-public r-rhisat2 (package (name "r-rhisat2") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 "0a7k9p08gq537275r7dfzh34ycxx8h4fmac74jimwhsa420793r5")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'make-reproducible (lambda _ (substitute* "src/Makefile" (("`hostname`") "guix") (("`date`") "0") ;; Avoid shelling out to "which". (("^CC =.*") (which "gcc")) (("^CPP =.*") (which "g++"))) #t))))) (propagated-inputs (list r-genomicranges r-sgseq r-txdbmaker)) (native-inputs (list r-knitr)) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description "This package provides an R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.") (license license:gpl3))) (define-public r-quasr (package (name "r-quasr") (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 "116qnp7d7z4a56fv6n55yzrdlmma9gwrw234nmy8iapkn5ms3xky")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biobase r-biocgenerics r-biocparallel r-biostrings r-bsgenome r-genomeinfodb r-genomicfeatures r-genomicfiles r-genomicranges r-iranges r-rbowtie r-rhtslib r-rsamtools r-rtracklayer r-s4vectors r-shortread r-txdbmaker)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description "This package provides a framework for the quantification and analysis of short genomic reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.") (license license:gpl2))) (define-public r-rqc (package (name "r-rqc") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 "0szd5ygcvpaiwqss8galxzxpslpfh93rk42s865v0qpv0s9v9x0l")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biocparallel r-biocstyle r-biostrings r-biovizbase r-genomicalignments r-genomicfiles r-ggplot2 r-iranges r-knitr r-markdown r-plyr r-rcpp r-reshape2 r-rsamtools r-s4vectors r-shiny r-shortread)) (native-inputs (list r-knitr)) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description "Rqc is an optimized tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.") (license license:gpl2+))) (define-public r-birewire (package (name "r-birewire") (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 "1l3hkq6n7i9j82aym4ngwablj8jqb70a7y6skx0rjkflya6wbim7")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix r-rtsne r-slam)) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description "This package provides functions for bipartite network rewiring through N consecutive switching steps and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. It includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections.") 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A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.") (license license:gpl2+))) (define-public r-multidataset (package (name "r-multidataset") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 "1y1j5svi52cvixjsn13122kvd0z0c7zfki3p6rr8wjd5w7riiyqw")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-ggplot2 r-ggrepel r-iranges r-limma r-qqman r-s4vectors r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description "This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. 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(license license:expat))) (define-public r-ropls (package (name "r-ropls") (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 "0cdkwzrbr6h1dfi3qdh629hi2jlm1hxgq4dvx4z3vc2r6w0c6m11")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-ggplot2 r-multiassayexperiment r-multidataset r-plotly r-summarizedexperiment)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") (synopsis "Multivariate analysis and feature selection of omics data") (description "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. This package provides imlementations of PCA, PLS, and OPLS for multivariate analysis and feature selection of omics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients).") 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The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.") (license license:cecill))) (define-public r-annotatr (package (name "r-annotatr") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 "11cc3nknbckm0v5r7dzgqzw0137w4c08ab10s9svb1y02z45a0qz")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-annotationhub r-dplyr r-genomeinfodb r-genomicfeatures r-genomicranges r-ggplot2 r-iranges r-readr r-regioner r-reshape2 r-rtracklayer r-s4vectors)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.") (license license:gpl3))) (define-public r-rsubread (package (name "r-rsubread") (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 "0nd5b1k0dsxpf93wqx01fgbvk40jcfs7b7w692bsx620lm42ipfg")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-matrix)) (home-page "https://bioconductor.org/packages/Rsubread/") (synopsis "Subread sequence alignment and counting for R") (description "This package provides tools for alignment, quantification and analysis of second and third generation sequencing data. It includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) (define-public r-flames (package (name "r-flames") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FLAMES" version)) (sha256 (base32 "1fcz0v1vy0q5zmdpawlk4a7fbqd01954p0jby9nbzgbk85hl16mi")))) (properties `((upstream-name . "FLAMES"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'fix-build-system (lambda _ ;; One target uses & instead of &&, which leads to a command ;; being run despite the check failing. 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Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.") (license license:gpl2+))) (define-public r-flowai (package (name "r-flowai") (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowAI" version)) (sha256 (base32 "1siqza92iak5lz38hbfznqndrmq995ihp6sbam0n2d3mj8vwv9qa")))) (properties `((upstream-name . "flowAI"))) (build-system r-build-system) (propagated-inputs (list r-changepoint r-flowcore r-ggplot2 r-knitr r-plyr r-rcolorbrewer r-reshape2 r-rmarkdown r-scales)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/flowAI") (synopsis "Automatic and interactive quality control for flow cytometry data") (description "This package is able to perform an automatic or interactive quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties: @enumerate @item flow rate @item signal acquisition, and @item dynamic range, @end enumerate the quality control enables the detection and removal of anomalies.") (license license:gpl2+))) (define-public r-flowutils (package (name "r-flowutils") (version "1.59.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-corpcor r-flowcore r-graph r-runit r-xml)) (home-page "https://github.com/jspidlen/flowUtils") (synopsis "Utilities for flow cytometry") (description "This package provides utilities for flow cytometry data.") (license license:artistic2.0))) (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 "0y91kz1n3byadk505432cnlj9dfiw521fgb460d6dmly9s0d9yif")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) (propagated-inputs (list r-all r-biobase r-cluster)) (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") (synopsis "Clustering algorithm") (description "This package provides an implementation of an algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) ;; This is the latest commit and it solves a bug from the latest release. (define-public r-cycombine (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1")) (package (name "r-cycombine") (version (git-version "0.2.6" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/biosurf/cyCombine") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm")))) (properties `((upstream-name . 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(define-public r-cytolib (package (name "r-cytolib") (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 "0nrj892jihi4fv58si3il42s0vyz3gm4gmb65kidkky63gmsy6iq")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (inputs (list openblas protobuf zlib)) (native-inputs (list r-knitr)) (propagated-inputs (list r-bh r-rhdf5lib r-rprotobuflib)) (home-page "https://bioconductor.org/packages/cytolib/") (synopsis "C++ infrastructure for working with gated cytometry") (description "This package provides the core data structure and API to represent and interact with gated cytometry data.") (license license:artistic2.0))) (define-public r-flowcore (package (name "r-flowcore") (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 "1zq3qypmzk9ld48r50fmygfdqwwyykii8l0l6gh5bdrdan760bfn")))) (properties `((upstream-name . 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"flowWorkspace"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics r-cpp11 r-cytolib r-data-table r-delayedarray r-dplyr r-flowcore r-ggplot2 r-graph r-matrixstats r-ncdfflow r-rbgl r-rgraphviz r-rhdf5lib r-rprotobuflib r-s4vectors r-scales r-xml)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description "This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.") (license license:artistic2.0))) (define-public r-flowstats (package (name "r-flowstats") (version "4.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 "0q8g3sqmbhinfrb63yhv4lsczjz7pqwhwwsdlz2cg7s8yhp0cj6v")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-clue r-cluster r-corpcor r-fda r-flowcore r-flowviz r-flowworkspace r-kernsmooth r-ks r-lattice r-mass r-mnormt r-ncdfflow r-rcolorbrewer r-rrcov)) (home-page "http://www.github.com/RGLab/flowStats") (synopsis "Statistical methods for the analysis of flow cytometry data") (description "This package provides methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the @code{flowCore} package.") (license license:artistic2.0))) (define-public r-opencyto (package (name "r-opencyto") (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 "13ndjvm3l5pl1jgv7bqp78didqq3rx6br4p1ncqqp68mm048f2ll")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics r-cpp11 r-data-table r-flowclust r-flowcore r-flowviz r-flowworkspace r-graph r-ncdfflow r-rbgl r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description "This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy.") (license license:artistic2.0))) (define-public r-cytoml (package (name "r-cytoml") (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 "11kflx3yahl7xjl6x2rgpd4hl5y69qgarzhalmz4qdci7b7ln7kr")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs (list libxml2)) (propagated-inputs (list r-bh r-biobase r-cpp11 r-cytolib r-data-table r-dplyr r-flowcore r-flowworkspace r-ggcyto r-graph r-jsonlite r-opencyto r-rbgl r-rgraphviz r-rhdf5lib r-rprotobuflib r-tibble r-xml r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/RGLab/CytoML") (synopsis "GatingML interface for cross platform cytometry data sharing") (description "This package provides an interface to implementations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.") (license license:artistic2.0))) (define-public r-flowsom (package (name "r-flowsom") (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 "0xqrp184p00pvzzf6ddmp2r8lpg97bm0q6smjwcrfb8rn4msxmis")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-colorramps r-consensusclusterplus r-dplyr r-flowcore r-ggforce r-ggnewscale r-ggplot2 r-ggpubr r-igraph r-magrittr r-rlang r-rtsne r-tidyr r-xml)) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") (description "FlowSOM offers visualization options for cytometry data, by using self-organizing map clustering and minimal spanning trees.") (license license:gpl2+))) (define-public r-mixomics (package (name "r-mixomics") (version "6.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 "03pdg2hz4wnyigqakb9098ak9ww8fhwypzn006hfad0s042p9wvj")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-corpcor r-dplyr r-ellipse r-ggplot2 r-ggrepel r-gridextra r-igraph r-lattice r-mass r-matrixstats r-rarpack r-rcolorbrewer r-reshape2 r-tidyr)) (native-inputs (list r-knitr)) (home-page "http://www.mixOmics.org") (synopsis "Multivariate methods for exploration of biological datasets") (description "mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data.") (license license:gpl2+))) (define-public r-depecher (package ;Source/Weave error (name "r-depecher") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 "15lpn1p2p28lhmzi7svszr0p1zkyaivi69q8pxcrv4lvips38hk4")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs (list r-beanplot r-clusterr r-collapse r-dosnow r-dplyr r-fnn r-foreach r-ggplot2 r-gmodels r-gplots r-mass r-matrixstats r-mixomics r-moments r-rcpp r-rcppeigen r-reshape2 r-robustbase r-viridis)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") (description "The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.") (license license:expat))) (define-public r-rcistarget (package (name "r-rcistarget") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 "1856jnvqacr12j5hnnl4w2abjjd7qvkz7cs8yhbnqpy1896wki0v")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs (list r-arrow r-aucell r-biocgenerics r-data-table r-dplyr r-genomeinfodb r-genomicranges r-gseabase r-r-utils r-s4vectors r-summarizedexperiment r-tibble r-zoo)) (native-inputs (list r-knitr)) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the @dfn{transcription start site} (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).") (license license:gpl3))) (define-public r-chicago (package (name "r-chicago") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 "05djywxsyfxb26d0clx51q7wmsw3rq56va444d6iy5n7xlhj9m94")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Chicago") (synopsis "Capture Hi-C analysis of genomic organization") (description "This package provides a pipeline for analysing Capture Hi-C data.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-ciara (package (name "r-ciara") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "CIARA" version)) (sha256 (base32 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf")))) (properties `((upstream-name . "CIARA"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=CIARA") (synopsis "Cluster-independent algorithm for rare cell types identification") (description "This is a package to support identification of markers of rare cell types by looking at genes whose expression is confined in small regions of the expression space.") (license license:artistic2.0))) (define-public r-cicero (package (name "r-cicero") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 "0x5ly5hkqli5b67hiaa6ha02damyps7vb4l51p0az1j5fxl39n8r")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-biobase r-biocgenerics r-data-table r-dplyr r-fnn r-genomicranges r-ggplot2 r-glasso r-gviz r-igraph r-iranges r-matrix r-monocle r-plyr r-reshape2 r-s4vectors r-stringi r-stringr r-tibble r-tidyr r-vgam)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description "Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data.") (license license:expat))) ;; This is the latest commit on the "monocle3" branch. (define-public r-cicero-monocle3 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") (revision "1")) (package (inherit r-cicero) (name "r-cicero-monocle3") (version (git-version "1.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/cole-trapnell-lab/cicero-release") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs (modify-inputs (package-propagated-inputs r-cicero) (delete "r-monocle") (prepend r-monocle3)))))) (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 "0gjnx4645kd7qag7dzs5dp9lhsv6zg5xn6jna3bap4mginl1jvxi")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) (propagated-inputs (list r-annotationhub r-biostrings r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-deseq2 r-dplyr r-edger r-genomeinfodb r-genomicranges r-ggplot2 r-gwascat r-iranges r-magrittr r-r-utils r-readr r-reshape2 r-rlang r-rtracklayer r-s4vectors r-seqinr r-stringi r-stringr r-universalmotif)) (native-inputs (list r-knitr)) (home-page "https://github.com/Aufiero/circRNAprofiler") (synopsis "Computational framework for the downstream analysis of circular RNA's") (description "@code{r-circrnaprofiler} is a computational framework for a comprehensive in silico analysis of @dfn{circular RNA} (circRNAs). This computational framework allows combining and analyzing circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.") (license license:gpl3))) (define-public r-cistopic (package (name "r-cistopic") (version "2.1.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aertslab/cisTopic") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf")))) (build-system r-build-system) (propagated-inputs (list r-aucell r-data-table r-dplyr r-dosnow r-dt r-feather r-fitdistrplus r-genomicranges r-ggplot2 r-lda r-matrix r-plyr r-rcistarget r-rtracklayer r-s4vectors)) (home-page "https://github.com/aertslab/cisTopic") (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") (description "The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as @dfn{Latent Dirichlet Allocation} (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single cell epigenomics data, and includes functionalities to identify cell states based on the contribution of cisTopics and explore the nature and regulatory proteins driving them.") (license license:gpl3))) (define-public r-cistopic-next (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803") (revision "1")) (package (inherit r-cistopic) (name "r-cistopic-next") ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd ;; since the previous release is 2.1.0. Oh well. (version (git-version "0.3.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aertslab/cisTopic") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2")))) (properties `((upstream-name . "cisTopic"))) (propagated-inputs (list r-aucell r-data-table r-dosnow r-dplyr r-dt r-feather r-fitdistrplus r-genomicranges r-ggplot2 r-lda r-matrix r-plyr r-rcistarget r-rtracklayer r-s4vectors r-text2vec)) (native-inputs (list r-knitr))))) (define-public r-genie3 (package (name "r-genie3") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 "0ijwyx42saqas52273c63c3yi948bh4pd4lifyqi3zjjs17bj1cg")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-reshape2)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/GENIE3") (synopsis "Gene network inference with ensemble of trees") (description "This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.") (license license:gpl2+))) (define-public r-roc (package (name "r-roc") (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 "074c6jg0dyr3hckizpg56f8ij8szj43cx6x5bbw7a01xdjdc70yb")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") (description "This package provides utilities for @dfn{Receiver Operating Characteristic} (ROC) curves, with a focus on micro arrays.") (license license:artistic2.0))) (define-public r-watermelon (package (name "r-watermelon") (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 "19zlv9aglllsjq3jcnlw994bkanjdq0ib46k7wjsig04cx4apz1v")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-illuminahumanmethylation450kanno-ilmn12-hg19 r-illuminaio r-limma r-lumi r-matrixstats r-methylumi r-roc)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/wateRmelon/") (synopsis "Illumina 450 methylation array normalization and metrics") (description "The standard index of DNA methylation (beta) is computed from methylated and unmethylated signal intensities. Betas calculated from raw signal intensities perform well, but using 11 methylomic datasets we demonstrate that quantile normalization methods produce marked improvement. The commonly used procedure of normalizing betas is inferior to the separate normalization of M and U, and it is also advantageous to normalize Type I and Type II assays separately. This package provides 15 flavours of betas and three performance metrics, with methods for objects produced by the @code{methylumi} and @code{minfi} packages.") (license license:gpl3))) (define-public r-gdsfmt (package (name "r-gdsfmt") (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 "0m5ws1qnbx7a3vj8bd9ggqi5w4icgzd5zi60qcy942j6zv4sswig")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. (snippet '(begin (for-each delete-file-recursively '("src/LZ4" "src/XZ" "src/ZLIB")) (substitute* "src/Makevars" (("all: \\$\\(SHLIB\\)") "all:") (("\\$\\(SHLIB\\): liblzma.a") "") (("^ (ZLIB|LZ4)/.*") "") (("CoreArray/dVLIntGDS.cpp.*") "CoreArray/dVLIntGDS.cpp") (("CoreArray/dVLIntGDS.o.*") "CoreArray/dVLIntGDS.o") (("PKG_LIBS = ./liblzma.a") "PKG_LIBS = -llz4")) (substitute* "src/CoreArray/dStream.h" (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) (string-append "include <" header ">"))))))) (properties `((upstream-name . "gdsfmt") (updater-extra-inputs . ("lz4" "xz" "zlib")))) (build-system r-build-system) (inputs (list lz4 xz zlib)) (native-inputs (list r-knitr)) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") (description "This package provides a high-level R interface to CoreArray @dfn{Genomic Data Structure} (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The @code{gdsfmt} package offers efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package @code{parallel}.") (license license:lgpl3))) (define-public r-bigmelon (package (name "r-bigmelon") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 "0fa1dwbk6hdiwg6dmbks7hy4cg3ydyd2sv94cyl0003awhf00nn9")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-gdsfmt r-geoquery r-illuminaio r-methylumi r-minfi r-watermelon)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description "This package provides methods for working with Illumina arrays using the @code{gdsfmt} package.") (license license:gpl3))) (define-public r-seqbias (package (name "r-seqbias") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 "18pdpi855y1hhka96xc5886nqffjn1jhz9jr9p305iikdrsvmjp1")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-genomicranges r-rhtslib r-zlibbioc)) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description "This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.") (license license:lgpl3))) (define-public r-reqon (package (name "r-reqon") (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 "0w28b3ma8r8rshijdm5jj1z64v91my7hcvw18r9pdwjprh05bw0g")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs (list r-rjava r-rsamtools r-seqbias)) (home-page "https://bioconductor.org/packages/ReQON/") (synopsis "Recalibrating quality of nucleotides") (description "This package provides an implementation of an algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.") (license license:gpl2))) (define-public r-wavcluster (package (name "r-wavcluster") (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 "0yr4jfaxs253xg5q0kds8fm97kqacx67pw1c80yx2w79v7nqskgv")))) (properties `((upstream-name . 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In addition, the package integrates RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. While wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).") (license license:gpl2))) (define-public r-tilingarray (package (name "r-tilingarray") (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tilingArray" version)) (sha256 (base32 "1408275gvfilc2k8sfsja8bm5fdgnblf2sf5wdd3if51qi61clb0")))) (properties `((upstream-name . 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Region-level statistics are obtained by fitting a @dfn{generalized least squares} (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.") (license license:expat))) (define-public r-omicade4 (package (name "r-omicade4") (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "omicade4" version)) (sha256 (base32 "18gp8qpmnbc5yjqyvvwvmrdybvm6zddc0r8bfglxz5wg4a91h4wk")))) (properties `((upstream-name . "omicade4"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-biobase r-made4)) (home-page "https://bioconductor.org/packages/omicade4") (synopsis "Multiple co-inertia analysis of omics datasets") (description "This package performes multiple co-inertia analysis of omics datasets.") 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It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data.") (license license:expat))) (define-public r-biscuiteer (package (name "r-biscuiteer") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 "15bisrcgyiv9ndfvgm0p4igyr4jwsf68ccis1nf1hi9x291k7m6y")))) (properties `((upstream-name . 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(license license:gpl3+))) (define-public r-tricycle (package (name "r-tricycle") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 "11928pcd8xzmll28m0ihi3rasc4w1i0fshn4bh9n2lyigkr5ayi4")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-circular r-dplyr r-genomicranges r-ggnewscale r-ggplot2 r-iranges r-rcolorbrewer r-s4vectors r-scater r-scattermore r-singlecellexperiment r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/hansenlab/tricycle") (synopsis "Transferable representation and inference of cell cycle") (description "The package contains functions to infer and visualize cell cycle process using Single-cell RNA-Seq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. The @code{tricycle} provides a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, it also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.") (license license:gpl3))) (define-public r-tximeta (package (name "r-tximeta") (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 "0lmkxl7zlp6z4i32jyy914kiwacnz89jnd2kqma81mq81r389p06")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-annotationhub r-biocfilecache r-biostrings r-ensembldb r-genomeinfodb r-genomicfeatures r-genomicranges r-iranges r-jsonlite r-matrix r-s4vectors r-summarizedexperiment r-tibble r-txdbmaker r-tximport)) (native-inputs (list r-knitr)) (home-page "https://github.com/mikelove/tximeta") (synopsis "Transcript quantification import with automatic metadata") (description "This package implements transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.") (license license:gpl2))) (define-public r-phyloseq (package (name "r-phyloseq") (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 (base32 "0a8q4wcqcxs7933bxg9bg03ps6hnybvcpqmlpz1pjy3affzghcbi")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-biobase r-biocgenerics r-biomformat r-biostrings r-cluster r-data-table r-foreach r-ggplot2 r-igraph r-multtest r-plyr r-reshape2 r-scales r-vegan)) (native-inputs (list r-knitr)) (home-page "https://github.com/joey711/phyloseq") (synopsis "Handling and analysis of high-throughput microbiome census data") (description "Phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.") (license license:agpl3))) ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar ;;; functionality or similar names. ;;;
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