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-rw-r--r--gnu/packages/bioconductor.scm668
1 files changed, 584 insertions, 84 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 74071900a3..c913232680 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -57,6 +57,7 @@
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
+ #:use-module (gnu packages tls)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module ((srfi srfi-1) #:hide (zip)))
@@ -1708,6 +1709,37 @@ gene expression indicate a role for enhancer priming in immune response\", publi
in Nature Genetics, January 2018.")
(license license:gpl2+)))
+(define-public r-mousegastrulationdata
+ (package
+ (name "r-mousegastrulationdata")
+ (version "1.14.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MouseGastrulationData" version
+ 'experiment))
+ (sha256
+ (base32
+ "155kci5isq7mlbvv8mdl2jjpafm3pbv1likhls70aa746spr1h17"))))
+ (properties `((upstream-name . "MouseGastrulationData")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biocgenerics
+ r-bumpymatrix
+ r-experimenthub
+ r-s4vectors
+ r-singlecellexperiment
+ r-spatialexperiment
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/MarioniLab/MouseGastrulationData")
+ (synopsis
+ "Single-Cell omics data across mouse gastrulation and early organogenesis")
+ (description
+ "This package provides processed and raw count data for single-cell RNA
+sequencing. In addition, this package offers single-cell ATAC-seq, and
+@code{seqFISH} (spatial transcriptomic) experiments performed along a
+timecourse of mouse gastrulation and early organogenesis.")
+ (license license:gpl3)))
+
(define-public r-minfidata
(package
(name "r-minfidata")
@@ -1754,6 +1786,38 @@ LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
files for various search engines.")
(license license:gpl2+)))
+(define-public r-msigdb
+ (package
+ (name "r-msigdb")
+ (version "1.8.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "msigdb" version
+ 'experiment))
+ (sha256
+ (base32
+ "1kgsqg1d5r852qas09g6fs0pcmk6jgbb6g983v6iqw19qsiy6jby"))))
+ (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")
@@ -1933,6 +1997,40 @@ cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and contro
;; The author(s) mentions only LGPL without any specific version.
(license license:lgpl2.1+)))
+(define-public r-sesamedata
+ (package
+ (name "r-sesamedata")
+ (version "1.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "sesameData" version
+ 'experiment))
+ (sha256
+ (base32
+ "1fvxs5n6bj2j0k3vgnaiksshkaxw7fmx6k22rjd3fsqg3cz60fm6"))))
+ (properties `((upstream-name . "sesameData")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-annotationhub
+ r-experimenthub
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-readr
+ r-s4vectors
+ r-stringr))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/sesameData")
+ (synopsis "Supporting Data for SeSAMe Package")
+ (description
+ "This package provides supporting annotation and test data for
+@code{SeSAMe} package. This includes chip tango addresses, mapping
+information, performance annotation, and trained predictor for Infinium array
+data. This package provides user access to essential annotation data for
+working with many generations of the Infinium DNA methylation array. It
+currently supports human array (HM27, HM450, EPIC), mouse array (MM285) and
+the @code{HorvathMethylChip40} (Mammal40) array.")
+ (license license:artistic2.0)))
+
(define-public r-tcgabiolinksgui-data
(package
(name "r-tcgabiolinksgui-data")
@@ -2923,13 +3021,13 @@ for use in Bioconductor’s AnnotationHub.")
(define-public r-anvil
(package
(name "r-anvil")
- (version "1.12.3")
+ (version "1.12.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnVIL" version))
(sha256
(base32
- "0dx10gcch6csk8nw3ffz4yvn5jf0v80ynsp3dg1az0ybkqyrzbih"))))
+ "05wgrr16vaqb7982j7nyri6rrhx90ljgxc37afhw190wc5dj07n0"))))
(properties `((upstream-name . "AnVIL")))
(build-system r-build-system)
(propagated-inputs
@@ -3357,6 +3455,44 @@ at @dfn{EBI} (European Bioinformatics Institute) and build Bioconductor data
structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
(license license:artistic2.0)))
+(define-public r-arrayqualitymetrics
+ (package
+ (name "r-arrayqualitymetrics")
+ (version "3.56.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "arrayQualityMetrics" version))
+ (sha256
+ (base32
+ "06plgmgla7hvryqfcid4y35s24r50s39d9f8sjchwbxqciwy72wj"))))
+ (properties `((upstream-name . "arrayQualityMetrics")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-affy
+ r-affyplm
+ r-beadarray
+ r-biobase
+ r-genefilter
+ r-gridsvg
+ r-hmisc
+ r-hwriter
+ r-lattice
+ r-latticeextra
+ r-limma
+ r-rcolorbrewer
+ r-setrng
+ r-svglite
+ r-vsn
+ r-xml))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/arrayQualityMetrics")
+ (synopsis "Quality metrics report for microarray data sets")
+ (description
+ "This package generates microarray quality metrics reports for data in
+Bioconductor microarray data containers @code{(ExpressionSet},
+@code{NChannelSet}, @code{AffyBatch}). One and two color array platforms are
+supported.")
+ (license license:lgpl2.0+)))
+
(define-public r-asafe
(package
(name "r-asafe")
@@ -3865,13 +4001,13 @@ Various visual and textual types of output are available.")
(define-public r-bambu
(package
(name "r-bambu")
- (version "3.2.5")
+ (version "3.2.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "bambu" version))
(sha256
(base32
- "1vqxmz2lknnx1g61y7skvznsnxv3clajngz9mnggg1z3p5mr6cnh"))))
+ "0h7ps32vbcn4hjpfb343nn8b50zq9my0k61847fi69vc4siwcx5k"))))
(properties `((upstream-name . "bambu")))
(build-system r-build-system)
(propagated-inputs
@@ -4797,13 +4933,13 @@ fold changes mean and variability for each selected gene.")
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.26.6")
+ (version "0.26.7")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "0jy2spqysa5x1s84kbr1jbbdmlh3q44lrw1qck2fln3b6q5vgz0k"))))
+ "1xsq85nm1gk537mw6ppsyykpw70kczv6wn1nll63b0k8xs4wj0ha"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
@@ -4831,13 +4967,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(define-public r-densvis
(package
(name "r-densvis")
- (version "1.10.2")
+ (version "1.10.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "densvis" version))
(sha256
(base32
- "0ypwnxi7ilczcvf5lwvyh6ck0jpvn1x90aggq66yqnn6yjy5md8s"))))
+ "1nkii02bj49z9qm3rj8lzwpz7dllrsa5zf7dn5ffcczyxr3b1ap9"))))
(properties `((upstream-name . "densvis")))
(build-system r-build-system)
(propagated-inputs (list r-assertthat r-basilisk r-irlba r-rcpp
@@ -4859,6 +4995,52 @@ space. This can help to create visualisations that are more representative of
heterogeneity in the original high-dimensional space.")
(license license:expat)))
+(define-public r-derfinder
+ (package
+ (name "r-derfinder")
+ (version "1.34.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "derfinder" version))
+ (sha256
+ (base32
+ "1gb65hk26ffn0njsgwgk43z9i9bcvx89pz5m9x951c2a07c1xrcw"))))
+ (properties `((upstream-name . "derfinder")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-annotationdbi
+ r-biocgenerics
+ r-biocparallel
+ r-bumphunter
+ r-derfinderhelper
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicfiles
+ r-genomicranges
+ r-hmisc
+ r-iranges
+ r-qvalue
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/lcolladotor/derfinder")
+ (synopsis
+ "Annotation-agnostic differential expression analysis of RNA-seq data")
+ (description
+ "This package provides functions for annotation-agnostic differential
+expression analysis of RNA-seq data. Two implementations of the DER Finder
+approach are included in this package:
+
+@enumerate
+@item single base-level F-statistics and
+@item DER identification at the expressed regions-level.
+@end enumerate
+
+The DER Finder approach can also be used to identify differentially bounded
+@code{ChIP-seq} peaks.")
+ (license license:artistic2.0)))
+
(define-public r-derfinderhelper
(package
(name "r-derfinderhelper")
@@ -4887,17 +5069,18 @@ calculation in parallel.")
(define-public r-dmrcate
(package
(name "r-dmrcate")
- (version "2.14.0")
+ (version "2.14.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DMRcate" version))
(sha256
(base32
- "1kcp0hgxnrcslphdqb25jsicif52r1sk8c7sn73jkdxy4n64idbm"))))
+ "1va60r297cl6xw5mc4nf9igfizqqzz7i5436x26iw4q35jcwlfjl"))))
(properties `((upstream-name . "DMRcate")))
(build-system r-build-system)
(propagated-inputs
- (list r-bsseq
+ (list r-biomart
+ r-bsseq
r-dss
r-edger
r-experimenthub
@@ -5485,14 +5668,14 @@ performing parallel computations on multicore machines.")
(define-public r-affy
(package
(name "r-affy")
- (version "1.78.1")
+ (version "1.78.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "affy" version))
(sha256
(base32
- "1xj8pnaa782k1hxaiba6mcsqr21bk8xz31916836jz5l9848zjsw"))))
+ "0zsr87zsw5rp5rgdiv1bbsi6fx6b7qzlgjirzczky6fmf4dqwgnm"))))
(build-system r-build-system)
(propagated-inputs
(list r-affyio
@@ -6642,13 +6825,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
(define-public r-dittoseq
(package
(name "r-dittoseq")
- (version "1.12.0")
+ (version "1.12.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "dittoSeq" version))
(sha256
(base32
- "0g5xxzd2xvh0m1fmyzzriwnrq1ckcmb95h9yl60h5w3c3ph22438"))))
+ "0gpgmy1yqgxvxiyrinxnn78w68w81ldqyhzwz3yxj2brlld6ycd1"))))
(properties `((upstream-name . "dittoSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -7011,13 +7194,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.36.1")
+ (version "1.36.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "1c3fgni846vjw152m4aklb8kwrwjw3rww116a2cbii70nr86p5qg"))))
+ "0bd46s7ch4j70n0snjf2nyx8gzkxn7d563jh5i3i0wzb647f5hbg"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
@@ -7101,13 +7284,13 @@ Commons RESTful service.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.52.1")
+ (version "1.52.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "166l0pzg00kaagg3adnx1xy5bgmv42lm06a47i30lh14dc0k79wq"))))
+ "0givyx77gvx24wgq180jsb2q1b8g4j49rs6bxdmd0l04a87hm9cr"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -7348,13 +7531,13 @@ Enrichment Analysis} (GSEA).")
(define-public r-gsva
(package
(name "r-gsva")
- (version "1.48.2")
+ (version "1.48.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GSVA" version))
(sha256
(base32
- "1y0dz9ayyrz4ylppa8f4m4b20yajzdl1sz4wpz8kcsfhh71ii64y"))))
+ "0ljfw65ray9ks8g55bfzn0c1w4412y4a7996zddywn5qj5pkjkfb"))))
(properties `((upstream-name . "GSVA")))
(build-system r-build-system)
(propagated-inputs (list r-biobase
@@ -7450,13 +7633,13 @@ the Human Protein Atlas project.")
(define-public r-raggedexperiment
(package
(name "r-raggedexperiment")
- (version "1.24.0")
+ (version "1.24.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "RaggedExperiment" version))
(sha256
(base32
- "1xs7dz5mkh9zs078g2a0izij8vxrwhzh7gyjglp057gicsca0hal"))))
+ "0aa886mmk1c5h1i3xnk4niq4ylrawpsn2f62hwmfj5dsyl8a36ka"))))
(properties `((upstream-name . "RaggedExperiment")))
(build-system r-build-system)
(propagated-inputs (list r-biocgenerics
@@ -7480,6 +7663,28 @@ from a @code{GRangesList} representation and provides a semblance of a
rectangular dataset.")
(license license:artistic2.0)))
+(define-public r-rdisop
+ (package
+ (name "r-rdisop")
+ (version "1.60.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rdisop" version))
+ (sha256
+ (base32
+ "02mj02sa9qxc6678irx7g3yzab4sa5sf4jkdjzsi9i6519xd7sa4"))))
+ (properties `((upstream-name . "Rdisop")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-rcpp))
+ (home-page "https://github.com/sneumann/Rdisop")
+ (synopsis "Decomposition of isotopic patterns")
+ (description
+ "This is a package for identification of metabolites using high precision
+mass spectrometry. MS peaks are used to derive a ranked list of sum formulae,
+alternatively for a given sum formula the theoretical isotope distribution can
+be calculated to search in MS peak lists.")
+ (license license:gpl2)))
+
(define-public r-rhtslib
(package
(name "r-rhtslib")
@@ -7578,6 +7783,37 @@ Shiny-based display methods for Bioconductor objects.")
@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
(license license:artistic2.0)))
+(define-public r-lea
+ (package
+ (name "r-lea")
+ (version "3.12.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "LEA" version))
+ (sha256
+ (base32
+ "1kxrrl8pxhaipmzsw8gs4gs8g8xbp8169z9f7bcpgrfapnawafm9"))))
+ (properties `((upstream-name . "LEA")))
+ (build-system r-build-system)
+ (native-inputs (list r-knitr))
+ (home-page "http://membres-timc.imag.fr/Olivier.Francois/LEA/index.htm")
+ (synopsis
+ "R package for landscape and ecological association studies")
+ (description
+ "LEA is an R package dedicated to population genomics, landscape genomics
+and genotype-environment association tests. LEA can run analyses of
+population structure and genome-wide tests for local adaptation, and also
+performs imputation of missing genotypes. The package includes statistical
+methods for estimating ancestry coefficients from large genotypic matrices and
+for evaluating the number of ancestral populations (snmf). It performs
+statistical tests using latent factor mixed models for identifying genetic
+polymorphisms that exhibit association with environmental gradients or
+phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset
+statistics based on new or predicted environments (@code{genetic.gap},
+@code{genetic.offset}). LEA is mainly based on optimized programs that can
+scale with the dimensions of large data sets.")
+ (license license:gpl3)))
+
(define-public r-lfa
(package
(name "r-lfa")
@@ -8980,6 +9216,51 @@ tab-delimited (tabix) files.")
"This package models a RESTful service as if it were a nested R list.")
(license license:artistic2.0)))
+(define-public r-rtcga
+ (package
+ (name "r-rtcga")
+ (version "1.30.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RTCGA" version))
+ (sha256
+ (base32
+ "1y7ciq1270dc1c9y490fygrsylyzwl52fqi1vj7r75hy3rnwnv25"))))
+ (properties `((upstream-name . "RTCGA")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-assertthat
+ r-data-table
+ r-dplyr
+ r-ggplot2
+ r-ggthemes
+ r-htmltools
+ r-knitr
+ r-purrr
+ r-rcurl
+ r-rmarkdown
+ r-rvest
+ r-scales
+ r-stringi
+ r-survival
+ r-survminer
+ r-viridis
+ r-xml
+ r-xml2))
+ (native-inputs (list r-knitr))
+ (home-page "https://rtcga.github.io/RTCGA/")
+ (synopsis "The Cancer Genome Atlas data integration")
+ (description
+ "The Cancer Genome Atlas (TCGA) Data Portal provides a platform for
+researchers to search, download, and analyze data sets generated by TCGA. It
+contains clinical information, genomic characterization data, and high level
+sequence analysis of the tumor genomes. The key is to understand genomics to
+improve cancer care. RTCGA package offers download and integration of the
+variety and volume of TCGA data using patient barcode key, what enables easier
+data possession. This may have an benefcial infuence on impact on development
+of science and improvement of patients treatment. Furthermore, RTCGA package
+transforms TCGA data to tidy form which is convenient to use.")
+ (license license:gpl2)))
+
(define-public r-rtcgatoolbox
(package
(name "r-rtcgatoolbox")
@@ -9023,13 +9304,13 @@ pre-processed data.")
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.60.0")
+ (version "1.60.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "0gy8df0ndq6nyly4b5h3kby8k77rc4j9n7zhnliryvirpr6alm9m"))))
+ "06z02sz8zjg2lxp2q4qwhvh6dsi6srirdmhcdvmi3as50nnjmzd8"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -9043,7 +9324,7 @@ pre-processed data.")
(native-inputs
(list pkg-config))
(inputs
- (list zlib))
+ (list openssl zlib))
(propagated-inputs
(list r-biocgenerics
r-biocio
@@ -9401,6 +9682,48 @@ sequence motif occurrences across a large set of sequences centred at a common
reference point and sorted by a user defined feature.")
(license license:gpl3+)))
+(define-public r-sesame
+ (package
+ (name "r-sesame")
+ (version "1.18.4")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "sesame" version))
+ (sha256
+ (base32
+ "1il33ygys6y72l8p3fhx301q16w9kylfy6w92b64n8gqkn6dmsmn"))))
+ (properties `((upstream-name . "sesame")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biocfilecache
+ r-biocparallel
+ r-dplyr
+ r-genomeinfodb
+ r-genomicranges
+ r-ggplot2
+ r-illuminaio
+ r-iranges
+ r-mass
+ r-preprocesscore
+ r-readr
+ r-reshape2
+ r-s4vectors
+ r-sesamedata
+ r-stringr
+ r-summarizedexperiment
+ r-tibble
+ r-wheatmap))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/zwdzwd/sesame")
+ (synopsis "Step-wise analysis of DNA Methylation BeadChips")
+ (description
+ "This package provides tools For analyzing Illumina Infinium DNA
+methylation arrays. @code{SeSAMe} provides utilities to support analyses of
+multiple generations of Infinium DNA methylation @code{BeadChips}, including
+preprocessing, quality control, visualization and inference. @code{SeSAMe}
+features accurate detection calling, intelligent inference of ethnicity, sex
+and advanced quality control routines.")
+ (license license:expat)))
+
(define-public r-shinymethyl
(package
(name "r-shinymethyl")
@@ -9608,6 +9931,72 @@ identifier translation via the GDC API.")
"This package implements widgets to provide user interfaces.")
(license license:artistic2.0)))
+(define-public r-trackviewer
+ (package
+ (name "r-trackviewer")
+ (version "1.36.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "trackViewer" version))
+ (sha256
+ (base32
+ "1ngfpd308y8i3vgv07cggk2azs64lsyyc9zfi3pz0gapr33ha6a1"))
+ (snippet
+ '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js"))))
+ (properties `((upstream-name . "trackViewer")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/htmlwidgets/lib/d3"
+ (let ((source (assoc-ref inputs "_"))
+ (target "d3.v4.min.js"))
+ (format #true "Processing ~a --> ~a~%"
+ source target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))))))))
+ (propagated-inputs (list r-annotationdbi
+ r-biocgenerics
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-graph
+ r-grimport
+ r-gviz
+ r-htmlwidgets
+ r-interactionset
+ r-iranges
+ r-plotrix
+ r-rgraphviz
+ r-rhdf5
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-scales
+ r-strawr))
+ (native-inputs
+ (list esbuild
+ r-knitr
+ (origin
+ (method url-fetch)
+ (uri "https://web.archive.org/web/20230428092426id_/\
+https://d3js.org/d3.v4.js")
+ (sha256
+ (base32
+ "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))
+ (home-page "https://bioconductor.org/packages/trackViewer")
+ (synopsis "Web interface for interactive multi-omics data analysis")
+ (description
+ "TrackViewer offers multi-omics analysis with web based tracks and
+lollipops. Visualize mapped reads along with annotation as track layers for
+NGS datasets such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and
+methylation data.")
+ (license license:gpl2+)))
+
(define-public r-transcriptr
(package
(name "r-transcriptr")
@@ -9788,13 +10177,13 @@ tools either included in speaq or available elsewhere on CRAN.")
(define-public r-spectra
(package
(name "r-spectra")
- (version "1.10.1")
+ (version "1.10.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Spectra" version))
(sha256
(base32
- "0vq5ha5m1vny7nrhgfmmkjd30zv0xaignp1a1m0xj08lnhkkmd69"))))
+ "1jrlfm6k6v4vhzl4lg6sa49yw35ds9x3v7iyc2cvbxqmpp5haila"))))
(properties `((upstream-name . "Spectra")))
(build-system r-build-system)
(propagated-inputs (list r-biocgenerics
@@ -9842,13 +10231,13 @@ Biology at
(define-public r-stringdb
(package
(name "r-stringdb")
- (version "2.12.0")
+ (version "2.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "STRINGdb" version))
(sha256
- (base32 "0mcp9zzbayz208b573ll69glz63b2pnrxsl900y9zd9crim6vck4"))))
+ (base32 "1c0m9k3gjmj160k8xyj2r60lpx4qgp7xibljfg8ljxr33f8aqyaz"))))
(properties `((upstream-name . "STRINGdb")))
(build-system r-build-system)
(propagated-inputs
@@ -10661,14 +11050,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
(define-public r-diffbind
(package
(name "r-diffbind")
- (version "3.10.0")
+ (version "3.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
- "1p5fxfpvjz85a2n1jsmj3niqzymnlsja9b53q2yxvj327qq58z8a"))))
+ "12frl2wfvfz4gpq4fjsmglqyqfxdk3zjbhqkc78rzylbw37xx3bf"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(propagated-inputs
@@ -10961,13 +11350,13 @@ rectangular layout tree built by ggtree with the grammar of ggplot2.")
(define-public r-ggpicrust2
(package
(name "r-ggpicrust2")
- (version "1.7.1")
+ (version "1.7.2")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpicrust2" version))
(sha256
(base32
- "0a4ykfybwx1qhgn7ic29dzigiazj248iihdr1597jxj505q21gay"))))
+ "0yk62cc0vmv6dyfiwvvbgpsqlvp1cw61db60153xvzmcdvd077cl"))))
(properties `((upstream-name . "ggpicrust2")))
(build-system r-build-system)
(propagated-inputs (list r-aldex2
@@ -11140,13 +11529,13 @@ enrichedGO (addGeneIDs).")
(define-public r-matrixgenerics
(package
(name "r-matrixgenerics")
- (version "1.12.2")
+ (version "1.12.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MatrixGenerics" version))
(sha256
(base32
- "1bzdhm2dj93xffla00hphxn45mpyn3cr8nv8d5xjqgx8j136biyy"))))
+ "07hrafzn3787vprdwdk3cfyhi8df7hjvxg9vq7ad8raqzb37lqil"))))
(properties
`((upstream-name . "MatrixGenerics")))
(build-system r-build-system)
@@ -11858,14 +12247,14 @@ multiplication.")
(define-public r-treeio
(package
(name "r-treeio")
- (version "1.24.2")
+ (version "1.24.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "treeio" version))
(sha256
(base32
- "0xjhyrqpr54aaj4han69ndkbmz5kwnf01adh80v2r8jc8jwdfy6m"))))
+ "0shm0mdqvsk5qipdqbz3251kks6ii1vpx1pph0ms271nzs6fcvif"))))
(properties `((upstream-name . "treeio")))
(build-system r-build-system)
(propagated-inputs
@@ -11924,14 +12313,14 @@ data.")
(define-public r-ggtree
(package
(name "r-ggtree")
- (version "3.8.0")
+ (version "3.8.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggtree" version))
(sha256
(base32
- "174bdjqvq51rpdyjlcwgbxfmkpsbz6m94ymmhmsq3x39xlcbrq7y"))))
+ "0l8llnvmg8k5qgag6vfgx1gdv0x46p3ypfz5apv23qhlbx4jfjja"))))
(properties `((upstream-name . "ggtree")))
(build-system r-build-system)
(propagated-inputs
@@ -12631,6 +13020,28 @@ required source code files from the official Leidenalg distribution and
several functions from the R igraph package.")
(license license:gpl3+))))
+(define-public r-sangerseqr
+ (package
+ (name "r-sangerseqr")
+ (version "1.36.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "sangerseqR" version))
+ (sha256
+ (base32
+ "0hhq5zsx4srd9ndr370m44f80qdlrqafjv1838wf65gzijffhfqb"))))
+ (properties `((upstream-name . "sangerseqR")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biostrings r-shiny r-stringr))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/sangerseqR")
+ (synopsis "Tools for Sanger Sequencing data in R")
+ (description
+ "This package contains several tools for analyzing Sanger Sequencing data
+files in R, including reading @file{.scf} and @file{.ab1} files, making
+basecalls and plotting chromatograms.")
+ (license license:gpl2)))
+
(define-public r-sanssouci
;; sansscouci doesn't have a (versioned) release yet.
;; This is the latest commit as of packaging for Guix.
@@ -12947,6 +13358,32 @@ to identify differentially methylated regions in epigenetic epidemiology
studies.")
(license license:artistic2.0)))
+(define-public r-bumpymatrix
+ (package
+ (name "r-bumpymatrix")
+ (version "1.8.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BumpyMatrix" version))
+ (sha256
+ (base32
+ "021xn5d08phmwv6g8a5d4ap5kcf5syhm6vpr784l4k54lflssr5i"))))
+ (properties `((upstream-name . "BumpyMatrix")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-iranges r-matrix r-s4vectors))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/BumpyMatrix")
+ (synopsis "Bumpy matrix of non-scalar objects")
+ (description
+ "This package provides a class and subclasses for storing non-scalar
+objects in matrix entries. This is akin to a ragged array but the raggedness
+is in the third dimension, much like a bumpy surface--hence the name. Of
+particular interest is the @code{BumpyDataFrameMatrix}, where each entry is a
+Bioconductor data frame. This allows us to naturally represent multivariate
+data in a format that is compatible with two-dimensional containers like the
+@code{SummarizedExperiment} and @code{MultiAssayExperiment} objects.")
+ (license license:expat)))
+
(define-public r-mia
(package
(name "r-mia")
@@ -13265,16 +13702,17 @@ and Infinium HD arrays are also included.")
(define-public r-lefser
(package
(name "r-lefser")
- (version "1.10.0")
+ (version "1.10.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "lefser" version))
(sha256
(base32
- "0wi70b4k7s0xj7bh46s0x0fckqc5qspzq8k4k913vg6cnhqgw2dd"))))
+ "1ifmbbsbyzcyvjni9ww27c9qsqliv7vj2rv9mg9c7gnqgbg6h2c4"))))
(properties `((upstream-name . "lefser")))
(build-system r-build-system)
- (propagated-inputs (list r-coin r-ggplot2 r-mass r-summarizedexperiment))
+ (propagated-inputs
+ (list r-coin 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")
@@ -13795,24 +14233,56 @@ implemented for discovering disease associations of high-throughput biological
data.")
(license license:artistic2.0)))
+(define-public r-enrichedheatmap
+ (package
+ (name "r-enrichedheatmap")
+ (version "1.30.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "EnrichedHeatmap" version))
+ (sha256
+ (base32
+ "18p2vjcg76rrjzjl03zgm4yxrgllbd42hg8rvsdbfb0s7brzr7ya"))))
+ (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 "1.20.0")
+ (version "1.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "enrichplot" version))
(sha256
(base32
- "10vmlw58hgzcpv2hlxk9ircza889vs9z01z575633qj0ivsczh0z"))))
+ "0yxnh5bmfcfsciwm852rbb707v9zbky3lsz2xsyyaapm5jjb6npk"))))
(build-system r-build-system)
(propagated-inputs
(list r-aplot
r-dose
+ r-ggnewscale
r-ggplot2
r-ggraph
- r-ggnewscale
r-ggtree
r-gosemsim
r-igraph
@@ -13835,6 +14305,33 @@ interpreting functional enrichment results obtained from ORA or GSEA analyses.
All the visualization methods are developed based on ggplot2 graphics.")
(license license:artistic2.0)))
+;; This is a CRAN package, but it depends on Bioconductor packages, so we
+;; added it here.
+(define-public r-classdiscovery
+ (package
+ (name "r-classdiscovery")
+ (version "3.4.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "ClassDiscovery" version))
+ (sha256
+ (base32
+ "06l7jvpcdynij05hb0ka33zpg7xdyqyzfzx24s0bnlspp83yc62s"))))
+ (properties `((upstream-name . "ClassDiscovery")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biobase r-cluster r-mclust r-oompabase r-oompadata))
+ (native-inputs
+ (list r-xtable)) ;for vignettes
+ (home-page "https://oompa.r-forge.r-project.org/")
+ (synopsis
+ "Classes and methods for \"Class Discovery\" with Microarrays or Proteomics")
+ (description
+ "This package defines classes for \"class discovery\" in the OOMPA project.
+Class discovery primarily consists of unsupervised clustering methods with
+attempts to assess their statistical significance.")
+ (license license:asl2.0)))
+
(define-public r-clusterprofiler
(package
(name "r-clusterprofiler")
@@ -16112,22 +16609,20 @@ of the analyses while minimizing technical noise.")
(define-public r-cytolib
(package
(name "r-cytolib")
- (version "2.12.0")
+ (version "2.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cytolib" version))
(sha256
(base32
- "0r58960jhq44qs6p0l0kd4iazflxdar7sc7m2xa7dwwl9zh5zm42"))))
+ "0mfv259k92vz0g7zv8zir2av2nlmx6na1f6q9zyj24s18m7mrkqz"))))
(properties `((upstream-name . "cytolib")))
(build-system r-build-system)
(native-inputs
(list r-knitr))
(propagated-inputs
- (list r-bh
- r-rhdf5lib
- r-rprotobuflib))
+ (list r-bh r-rhdf5lib r-rprotobuflib))
(home-page "https://bioconductor.org/packages/cytolib/")
(synopsis "C++ infrastructure for working with gated cytometry")
(description
@@ -16138,14 +16633,14 @@ interact with gated cytometry data.")
(define-public r-flowcore
(package
(name "r-flowcore")
- (version "2.12.1")
+ (version "2.12.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowCore" version))
(sha256
(base32
- "09jirhhf1qfanyhbq1ybmw6smv8163b7cqgj0qw69grvs8bb0b6m"))))
+ "1z3xsp1ymvdjhwcj5mkhl1d586rlr5i8vji9y5gs595w3naa4r0h"))))
(properties `((upstream-name . "flowCore")))
(build-system r-build-system)
(propagated-inputs
@@ -16223,14 +16718,14 @@ manipulation of flow cytometry data.")
(define-public r-ggcyto
(package
(name "r-ggcyto")
- (version "1.28.0")
+ (version "1.28.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggcyto" version))
(sha256
(base32
- "1b2xsn0avm6r4zylygdhab3zz3v8qvwbm1xr58894dwgysdk8zc5"))))
+ "1hgw8g0b62k2lyswp3m81qczzwsyid7zdrnyjvl9388k29w2105s"))))
(properties `((upstream-name . "ggcyto")))
(build-system r-build-system)
(propagated-inputs
@@ -16325,14 +16820,14 @@ model with Box-Cox transformation.")
(define-public r-rprotobuflib
(package
(name "r-rprotobuflib")
- (version "2.12.0")
+ (version "2.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RProtoBufLib" version))
(sha256
(base32
- "0qlb3fp4lj3wys2hgrdrccfdf0lf85qnk0g117n959mg3y0dqikq"))))
+ "097nxjijblqyz6nbpal7292qfijmk7x8dbx7plryr132xbaw5hdm"))))
(properties `((upstream-name . "RProtoBufLib")))
(build-system r-build-system)
(arguments
@@ -16354,14 +16849,14 @@ for other R packages to compile and link against.")
(define-public r-flowworkspace
(package
(name "r-flowworkspace")
- (version "4.12.0")
+ (version "4.12.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowWorkspace" version))
(sha256
(base32
- "1ln98xnnqlz3hqdyhypzarw7jcghd5gjaw8h42yw41w0plhh4wyr"))))
+ "1g1hym2anysgy7v46fnnxyzac3wzi1713vlih2gqzi23k8r2xx26"))))
(properties `((upstream-name . "flowWorkspace")))
(build-system r-build-system)
(propagated-inputs
@@ -17720,14 +18215,14 @@ using whole genome sequencing data.")
(define-public r-activepathways
(package
(name "r-activepathways")
- (version "1.1.1")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ActivePathways" version))
(sha256
(base32
- "1crq164vyqhdq5y3q09k3m5zljqrhcd5ak0jrc0xqvzf0pasml2m"))))
+ "1niwzbzqs1s0mx6ia8fmvg9db6kajs0rdxgnnn1pq68yd8rjn79g"))))
(properties
`((upstream-name . "ActivePathways")))
(build-system r-build-system)
@@ -18406,13 +18901,13 @@ functionality.")
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.68.1")
+ (version "1.68.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "04rzrwxd9n4l3agmbkx03hhcmy2fx049q5n4glld46mvx3vjvc48"))))
+ "1icnaj1ifndym7nl1yafzd0y0fxyhzjyb4qzqpcnsqhh4yi3pnm5"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
@@ -18605,14 +19100,14 @@ gene selection, testing relationships, and so on.")
(define-public r-biocpkgtools
(package
(name "r-biocpkgtools")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocPkgTools" version))
(sha256
(base32
- "0s51dd9kjlh5vckwmynvahvg1pzl2ddvfn3s2kz77m0l0nbh7zfx"))
+ "16d0sjkzagc0jxha28qxplg6iihwg2q05sig0s1291lm7kh5k9j8"))
(snippet
'(for-each delete-file
'("inst/htmlwidgets/lib/bioc_explore/bootstrap.min.js"
@@ -18962,14 +19457,14 @@ truncated data.")
(define-public r-interval
(package
(name "r-interval")
- (version "1.1-0.8")
+ (version "1.1-1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "interval" version))
(sha256
(base32
- "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
+ "0kmz7wpgc4kspr11l0nls4rq0qk2lbsg3s4bpl0zs4r4pjcrwvrx"))))
(properties `((upstream-name . "interval")))
(build-system r-build-system)
(propagated-inputs
@@ -19081,17 +19576,22 @@ routines.")
(define-public r-s4arrays
(package
(name "r-s4arrays")
- (version "1.0.4")
+ (version "1.0.5")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Arrays" version))
(sha256
(base32
- "1pwkbp94r8vv43vgxcgqzbs1njhqlahfgsbf8rhr0ndy1bjyly2g"))))
+ "01xlccybhdgas9pnx88ll9q56qb2xd687xvfrc7bd5r9sf72b81c"))))
(properties `((upstream-name . "S4Arrays")))
(build-system r-build-system)
(propagated-inputs
- (list r-biocgenerics r-crayon r-iranges r-matrix r-s4vectors))
+ (list r-abind
+ r-biocgenerics
+ r-crayon
+ r-iranges
+ r-matrix
+ r-s4vectors))
(native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/S4Arrays")
(synopsis "Foundation of array-like containers in Bioconductor")
@@ -19783,14 +20283,14 @@ cell types to infer the cell of origin of each single cell independently.")
(define-public r-scuttle
(package
(name "r-scuttle")
- (version "1.10.1")
+ (version "1.10.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scuttle" version))
(sha256
(base32
- "13207k7b9qrpcngk4vd3jhc3zz815anwci1dqgadjyn4c8ragmnj"))))
+ "0225fk3ca540b9z3dd5q2zngxsa524nq7zrv1z5qnmr2knc0yxfb"))))
(properties `((upstream-name . "scuttle")))
(build-system r-build-system)
(propagated-inputs
@@ -19863,14 +20363,14 @@ quality control.")
(define-public r-scran
(package
(name "r-scran")
- (version "1.28.1")
+ (version "1.28.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "1qfmxarw5x17ag66r9i51vxm5h8fxm4rdicv6s8q5pnaf188hdcp"))))
+ "1la55s14frvsjp8ly02fbrkzvv7lzvcd7jc1axmwh494b9zy5jmd"))))
(build-system r-build-system)
(propagated-inputs
(list r-beachmat
@@ -19963,14 +20463,14 @@ Visium platform.")
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
- (version "1.22.1")
+ (version "1.22.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DelayedMatrixStats" version))
(sha256
(base32
- "13iqlw74zh65y2ckwg0b3xbqc6jgj34xjgsg9axfv7j7znwk9igg"))))
+ "1bzbsfds5zki6iazj53y6kps8bvn7zdysbmpf9359sv6zshk18fv"))))
(properties
`((upstream-name . "DelayedMatrixStats")))
(build-system r-build-system)
@@ -20414,14 +20914,14 @@ family of feature/genome hypotheses.")
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.44.0")
+ (version "1.44.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "1lp345hxlddsc91lxrzay073g2dabc8h1cynyh87y85vzffhwplw"))))
+ "0yfmpxvx7h344fp6i3iny7r61n904bj0qdy14qbsp3d0z4g8a5fn"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
@@ -21405,14 +21905,14 @@ using aCGH or sequencing.")
(define-public r-bionero
(package
(name "r-bionero")
- (version "1.8.5")
+ (version "1.8.7")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioNERO" version))
(sha256
(base32
- "0nrvq6cn55qzp66pqssyfxl2wh5dfqndchcv8qgfqajsnz8i35xm"))))
+ "0yvd05yikvblnhimnmn4srcsimab4qml5k582n0c9h4rppffmvy4"))))
(properties `((upstream-name . "BioNERO")))
(build-system r-build-system)
(propagated-inputs
@@ -21726,14 +22226,14 @@ fragments by exact matching.")
(define-public r-dmrseq
(package
(name "r-dmrseq")
- (version "1.20.0")
+ (version "1.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "dmrseq" version))
(sha256
(base32
- "1xj23dqvmxi1sn4qn4zwvn9ggv128kr3gxmd7906463s9ap8qjja"))))
+ "1lxrirgy42xnpdj7b2nrabbki33an8ri6j1mgxp3jn4h0a88c280"))))
(properties `((upstream-name . "dmrseq")))
(build-system r-build-system)
(propagated-inputs
@@ -21992,14 +22492,14 @@ embeddings and functions to build new reference.")
(define-public r-tximeta
(package
(name "r-tximeta")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "tximeta" version))
(sha256
(base32
- "03dmnpfffj18c6009qg985i596l4ckf3myin12g2p6xr56880bz1"))))
+ "02240v41scaqxabjb62zh6shkkzb9520dhn0lfc2jbimnb26yj7f"))))
(properties `((upstream-name . "tximeta")))
(build-system r-build-system)
(propagated-inputs
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