;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
+;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
-;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
+;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
;;;
;;; This file is part of GNU Guix.
;;;
in Biostrings objects.")
(license license:artistic2.0)))
+(define-public r-genomeinfodbdata
+ (package
+ (name "r-genomeinfodbdata")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
+ (sha256
+ (base32
+ "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
+ (properties
+ `((upstream-name . "GenomeInfoDbData")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
+ (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
+ (description "This package contains data for mapping between NCBI taxonomy
+ID and species. It is used by functions in the GenomeInfoDb package.")
+ (license license:artistic2.0)))
+
(define-public r-homo-sapiens
(package
(name "r-homo-sapiens")
"This package exposes an annotation database generated from Ensembl.")
(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
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-genomicfeatures" ,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")
from Illumina 450k methylation arrays.")
(license license:artistic2.0)))
+(define-public r-chromstardata
+ (package
+ (name "r-chromstardata")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "chromstaRData" version 'experiment))
+ (sha256
+ (base32
+ "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
+ (properties `((upstream-name . "chromstaRData")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/chromstaRData/")
+ (synopsis "ChIP-seq data for demonstration purposes")
+ (description
+ "This package provides ChIP-seq data for demonstration purposes in the
+chromstaR package.")
+ (license license:gpl3)))
+
(define-public r-genelendatabase
(package
(name "r-genelendatabase")
(properties `((upstream-name . "gageData")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/gageData")
- (synopsis "Auxillary data for gage package")
+ (synopsis "Auxiliary data for the gage package")
(description
"This is a supportive data package for the software package @code{gage}.
However, the data supplied here are also useful for gene set or pathway
used visualizations.")
(license license:artistic2.0)))
+(define-public r-delayedarray
+ (package
+ (name "r-delayedarray")
+ (version "0.16.3")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DelayedArray" version))
+ (sha256
+ (base32
+ "0w1wppy6m2iv41852dscg3y19sq84ahdx3m7c2p2pxjcznmv6hys"))))
+ (properties
+ `((upstream-name . "DelayedArray")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-matrixgenerics" ,r-matrixgenerics)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/DelayedArray")
+ (synopsis "Delayed operations on array-like objects")
+ (description
+ "Wrapping an array-like object (typically an on-disk object) in a
+@code{DelayedArray} object allows one to perform common array operations on it
+without loading the object in memory. In order to reduce memory usage and
+optimize performance, operations on the object are either delayed or executed
+using a block processing mechanism. Note that this also works on in-memory
+array-like objects like @code{DataFrame} objects (typically with Rle columns),
+@code{Matrix} objects, and ordinary arrays and data frames.")
+ (license license:artistic2.0)))
+
(define-public r-bluster
(package
(name "r-bluster")
arbitrary genomic intervals along chromosomal ideogram.")
(license license:gpl2)))
+(define-public r-iranges
+ (package
+ (name "r-iranges")
+ (version "2.24.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "IRanges" version))
+ (sha256
+ (base32
+ "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52"))))
+ (properties
+ `((upstream-name . "IRanges")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/IRanges")
+ (synopsis "Infrastructure for manipulating intervals on sequences")
+ (description
+ "This package provides efficient low-level and highly reusable S4 classes
+for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
+generally, data that can be organized sequentially (formally defined as
+@code{Vector} objects), as well as views on these @code{Vector} objects.
+Efficient list-like classes are also provided for storing big collections of
+instances of the basic classes. All classes in the package use consistent
+naming and share the same rich and consistent \"Vector API\" as much as
+possible.")
+ (license license:artistic2.0)))
+
+;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
+(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
+ `(("r-biobase" ,r-biobase)
+ ("r-deseq" ,r-deseq)
+ ("r-limma" ,r-limma)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,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 "1.0.4")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "BisqueRNA" version))
+ (sha256
+ (base32
+ "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
+ (properties `((upstream-name . "BisqueRNA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-limsolve" ,r-limsolve)))
+ (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
(define-public r-annotate
(package
- (name "r-annotate")
- (version "1.68.0")
+ (name "r-annotate")
+ (version "1.68.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "annotate" version))
+ (sha256
+ (base32
+ "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-dbi" ,r-dbi)
+ ("r-httr" ,r-httr)
+ ("r-xml" ,r-xml)
+ ("r-xtable" ,r-xtable)))
+ (home-page
+ "https://bioconductor.org/packages/annotate")
+ (synopsis "Annotation for microarrays")
+ (description "This package provides R environments for the annotation of
+microarrays.")
+ (license license:artistic2.0)))
+
+(define-public r-annotationdbi
+ (package
+ (name "r-annotationdbi")
+ (version "1.52.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationDbi" version))
+ (sha256
+ (base32
+ "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr"))))
+ (properties
+ `((upstream-name . "AnnotationDbi")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-dbi" ,r-dbi)
+ ("r-iranges" ,r-iranges)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/AnnotationDbi")
+ (synopsis "Annotation database interface")
+ (description
+ "This package provides user interface and database connection code for
+annotation data packages using SQLite data storage.")
+ (license license:artistic2.0)))
+
+(define-public r-annotationforge
+ (package
+ (name "r-annotationforge")
+ (version "1.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationForge" version))
+ (sha256
+ (base32
+ "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
+ (properties
+ `((upstream-name . "AnnotationForge")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-dbi" ,r-dbi)
+ ("r-rcurl" ,r-rcurl)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xml" ,r-xml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/AnnotationForge")
+ (synopsis "Code for building annotation database packages")
+ (description
+ "This package provides code for generating Annotation packages and their
+databases. Packages produced are intended to be used with AnnotationDbi.")
+ (license license:artistic2.0)))
+
+(define-public r-biobase
+ (package
+ (name "r-biobase")
+ (version "2.50.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Biobase" version))
+ (sha256
+ (base32
+ "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4"))))
+ (properties
+ `((upstream-name . "Biobase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)))
+ (home-page "https://bioconductor.org/packages/Biobase")
+ (synopsis "Base functions for Bioconductor")
+ (description
+ "This package provides functions that are needed by many other packages
+on Bioconductor or which replace R functions.")
+ (license license:artistic2.0)))
+
+(define-public r-biomart
+ (package
+ (name "r-biomart")
+ (version "2.46.3")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biomaRt" version))
+ (sha256
+ (base32
+ "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7"))))
+ (properties
+ `((upstream-name . "biomaRt")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocfilecache" ,r-biocfilecache)
+ ("r-httr" ,r-httr)
+ ("r-openssl" ,r-openssl)
+ ("r-progress" ,r-progress)
+ ("r-rappdirs" ,r-rappdirs)
+ ("r-stringr" ,r-stringr)
+ ("r-xml" ,r-xml)
+ ("r-xml2" ,r-xml2)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/biomaRt")
+ (synopsis "Interface to BioMart databases")
+ (description
+ "biomaRt provides an interface to a growing collection of databases
+implementing the @url{BioMart software suite, http://www.biomart.org}. The
+package enables retrieval of large amounts of data in a uniform way without
+the need to know the underlying database schemas or write complex SQL queries.
+Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
+Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
+users direct access to a diverse set of data and enable a wide range of
+powerful online queries from gene annotation to database mining.")
+ (license license:artistic2.0)))
+
+(define-public r-biocparallel
+ (package
+ (name "r-biocparallel")
+ (version "1.24.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocParallel" version))
+ (sha256
+ (base32
+ "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism"))))
+ (properties
+ `((upstream-name . "BiocParallel")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'make-reproducible
+ (lambda _
+ ;; Remove generated documentation.
+ (for-each delete-file
+ '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
+ "inst/doc/Introduction_To_BiocParallel.pdf"
+ "inst/doc/Errors_Logs_And_Debugging.pdf"
+ "inst/doc/BiocParallel_BatchtoolsParam.R"
+ "inst/doc/Introduction_To_BiocParallel.R"
+ "inst/doc/Errors_Logs_And_Debugging.R"))
+
+ ;; Remove time-dependent macro
+ (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
+ "inst/doc/Introduction_To_BiocParallel.Rnw"
+ "inst/doc/Errors_Logs_And_Debugging.Rnw"
+ "vignettes/BiocParallel_BatchtoolsParam.Rnw"
+ "vignettes/Introduction_To_BiocParallel.Rnw"
+ "vignettes/Errors_Logs_And_Debugging.Rnw")
+ (("\\today") "later"))
+
+ ;; Initialize the random number generator seed when building.
+ (substitute* "R/internal_rng_stream.R"
+ (("\"L'Ecuyer-CMRG\"\\)" m)
+ (string-append
+ m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
+ (propagated-inputs
+ `(("r-futile-logger" ,r-futile-logger)
+ ("r-snow" ,r-snow)
+ ("r-bh" ,r-bh)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/BiocParallel")
+ (synopsis "Bioconductor facilities for parallel evaluation")
+ (description
+ "This package provides modified versions and novel implementation of
+functions for parallel evaluation, tailored to use with Bioconductor
+objects.")
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-biostrings
+ (package
+ (name "r-biostrings")
+ (version "2.58.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Biostrings" version))
+ (sha256
+ (base32
+ "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5"))))
+ (properties
+ `((upstream-name . "Biostrings")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-crayon" ,r-crayon)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/Biostrings")
+ (synopsis "String objects and algorithms for biological sequences")
+ (description
+ "This package provides memory efficient string containers, string
+matching algorithms, and other utilities, for fast manipulation of large
+biological sequences or sets of sequences.")
+ (license license:artistic2.0)))
+
+(define-public r-category
+ (package
+ (name "r-category")
+ (version "2.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Category" version))
+ (sha256
+ (base32
+ "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
+ (properties `((upstream-name . "Category")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genefilter" ,r-genefilter)
+ ("r-graph" ,r-graph)
+ ("r-gseabase" ,r-gseabase)
+ ("r-matrix" ,r-matrix)
+ ("r-rbgl" ,r-rbgl)
+ ("r-dbi" ,r-dbi)))
+ (home-page "https://bioconductor.org/packages/Category")
+ (synopsis "Category analysis")
+ (description
+ "This package provides a collection of tools for performing category
+analysis.")
+ (license license:artistic2.0)))
+
+(define-public r-deseq2
+ (package
+ (name "r-deseq2")
+ (version "1.30.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DESeq2" version))
+ (sha256
+ (base32
+ "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19"))))
+ (properties `((upstream-name . "DESeq2")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-locfit" ,r-locfit)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/DESeq2")
+ (synopsis "Differential gene expression analysis")
+ (description
+ "This package provides functions to estimate variance-mean dependence in
+count data from high-throughput nucleotide sequencing assays and test for
+differential expression based on a model using the negative binomial
+distribution.")
+ (license license:lgpl3+)))
+
+(define-public r-dexseq
+ (package
+ (name "r-dexseq")
+ (version "1.36.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DEXSeq" version))
+ (sha256
+ (base32
+ "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
+ (properties `((upstream-name . "DEXSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biomart" ,r-biomart)
+ ("r-deseq2" ,r-deseq2)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-statmod" ,r-statmod)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/DEXSeq")
+ (synopsis "Inference of differential exon usage in RNA-Seq")
+ (description
+ "This package is focused on finding differential exon usage using RNA-seq
+exon counts between samples with different experimental designs. It provides
+functions that allows the user to make the necessary statistical tests based
+on a model that uses the negative binomial distribution to estimate the
+variance between biological replicates and generalized linear models for
+testing. The package also provides functions for the visualization and
+exploration of the results.")
+ (license license:gpl3+)))
+
+(define-public r-edger
+ (package
+ (name "r-edger")
+ (version "3.32.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "edgeR" version))
+ (sha256
+ (base32
+ "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
+ (properties `((upstream-name . "edgeR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-limma" ,r-limma)
+ ("r-locfit" ,r-locfit)
+ ("r-rcpp" ,r-rcpp)
+ ("r-statmod" ,r-statmod))) ;for estimateDisp
+ (home-page "http://bioinf.wehi.edu.au/edgeR")
+ (synopsis "EdgeR does empirical analysis of digital gene expression data")
+ (description "This package can do differential expression analysis of
+RNA-seq expression profiles with biological replication. It implements a range
+of statistical methodology based on the negative binomial distributions,
+including empirical Bayes estimation, exact tests, generalized linear models
+and quasi-likelihood tests. It be applied to differential signal analysis of
+other types of genomic data that produce counts, including ChIP-seq, SAGE and
+CAGE.")
+ (license license:gpl2+)))
+
+(define-public r-genefilter
+ (package
+ (name "r-genefilter")
+ (version "1.72.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "genefilter" version))
+ (sha256
+ (base32
+ "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("r-knitr" ,r-knitr)))
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-survival" ,r-survival)))
+ (home-page "https://bioconductor.org/packages/genefilter")
+ (synopsis "Filter genes from high-throughput experiments")
+ (description
+ "This package provides basic functions for filtering genes from
+high-throughput sequencing experiments.")
+ (license license:artistic2.0)))
+
+(define-public r-genomeinfodb
+ (package
+ (name "r-genomeinfodb")
+ (version "1.26.6")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomeInfoDb" version))
+ (sha256
+ (base32
+ "1wy4dwiv0pgim975var802z565py4a0nakx6zdvbhry4c0dfczd1"))))
+ (properties
+ `((upstream-name . "GenomeInfoDb")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomeinfodbdata" ,r-genomeinfodbdata)
+ ("r-iranges" ,r-iranges)
+ ("r-rcurl" ,r-rcurl)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/GenomeInfoDb")
+ (synopsis "Utilities for manipulating chromosome identifiers")
+ (description
+ "This package contains data and functions that define and allow
+translation between different chromosome sequence naming conventions (e.g.,
+\"chr1\" versus \"1\"), including a function that attempts to place sequence
+names in their natural, rather than lexicographic, order.")
+ (license license:artistic2.0)))
+
+(define-public r-genomicranges
+ (package
+ (name "r-genomicranges")
+ (version "1.42.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicRanges" version))
+ (sha256
+ (base32
+ "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i"))))
+ (properties
+ `((upstream-name . "GenomicRanges")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/GenomicRanges")
+ (synopsis "Representation and manipulation of genomic intervals")
+ (description
+ "This package provides tools to efficiently represent and manipulate
+genomic annotations and alignments is playing a central role when it comes to
+analyzing high-throughput sequencing data (a.k.a. NGS data). The
+GenomicRanges package defines general purpose containers for storing and
+manipulating genomic intervals and variables defined along a genome.")
+ (license license:artistic2.0)))
+
+(define-public r-gostats
+ (package
+ (name "r-gostats")
+ (version "2.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GOstats" version))
+ (sha256
+ (base32
+ "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
+ (properties `((upstream-name . "GOstats")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationforge" ,r-annotationforge)
+ ("r-biobase" ,r-biobase)
+ ("r-category" ,r-category)
+ ("r-go-db" ,r-go-db)
+ ("r-graph" ,r-graph)
+ ("r-rgraphviz" ,r-rgraphviz)
+ ("r-rbgl" ,r-rbgl)))
+ (home-page "https://bioconductor.org/packages/GOstats")
+ (synopsis "Tools for manipulating GO and microarrays")
+ (description
+ "This package provides a set of tools for interacting with GO and
+microarray data. A variety of basic manipulation tools for graphs, hypothesis
+testing and other simple calculations.")
+ (license license:artistic2.0)))
+
+(define-public r-gseabase
+ (package
+ (name "r-gseabase")
+ (version "1.52.1")
(source
(origin
(method url-fetch)
- (uri (bioconductor-uri "annotate" version))
+ (uri (bioconductor-uri "GSEABase" version))
(sha256
(base32
- "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
+ "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
+ (properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
- ("r-dbi" ,r-dbi)
- ("r-httr" ,r-httr)
- ("r-xml" ,r-xml)
- ("r-xtable" ,r-xtable)))
- (home-page
- "https://bioconductor.org/packages/annotate")
- (synopsis "Annotation for microarrays")
- (description "This package provides R environments for the annotation of
-microarrays.")
+ ("r-graph" ,r-graph)
+ ("r-xml" ,r-xml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/GSEABase")
+ (synopsis "Gene set enrichment data structures and methods")
+ (description
+ "This package provides classes and methods to support @dfn{Gene Set
+Enrichment Analysis} (GSEA).")
(license license:artistic2.0)))
(define-public r-hpar
the Human Protein Atlas project.")
(license license:artistic2.0)))
+(define-public r-limma
+ (package
+ (name "r-limma")
+ (version "3.46.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "limma" version))
+ (sha256
+ (base32
+ "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz"))))
+ (build-system r-build-system)
+ (home-page "http://bioinf.wehi.edu.au/limma")
+ (synopsis "Package for linear models for microarray and RNA-seq data")
+ (description "This package can be used for the analysis of gene expression
+studies, especially the use of linear models for analysing designed experiments
+and the assessment of differential expression. The analysis methods apply to
+different technologies, including microarrays, RNA-seq, and quantitative PCR.")
+ (license license:gpl2+)))
+
+(define-public r-rbgl
+ (package
+ (name "r-rbgl")
+ (version "1.66.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RBGL" version))
+ (sha256
+ (base32
+ "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
+ (properties `((upstream-name . "RBGL")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-graph" ,r-graph)))
+ (home-page "https://www.bioconductor.org/packages/RBGL")
+ (synopsis "Interface to the Boost graph library")
+ (description
+ "This package provides a fairly extensive and comprehensive interface to
+the graph algorithms contained in the Boost library.")
+ (license license:artistic2.0)))
+
(define-public r-regioner
(package
(name "r-regioner")
(define-public r-reportingtools
(package
(name "r-reportingtools")
- (version "2.30.0")
+ (version "2.30.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ReportingTools" version))
(sha256
(base32
- "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31"))))
+ "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb"))))
(properties
`((upstream-name . "ReportingTools")))
(build-system r-build-system)
browser.")
(license license:artistic2.0)))
+(define-public r-rsamtools
+ (package
+ (name "r-rsamtools")
+ (version "2.6.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rsamtools" version))
+ (sha256
+ (base32
+ "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554"))))
+ (properties
+ `((upstream-name . "Rsamtools")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-zlib
+ (lambda _
+ (substitute* "DESCRIPTION"
+ (("zlibbioc, ") ""))
+ (substitute* "NAMESPACE"
+ (("import\\(zlibbioc\\)") ""))
+ #t)))))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bitops" ,r-bitops)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
+ (synopsis "Interface to samtools, bcftools, and tabix")
+ (description
+ "This package provides an interface to the @code{samtools},
+@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
+Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
+tab-delimited (tabix) files.")
+ (license license:expat)))
+
+(define-public r-shortread
+ (package
+ (name "r-shortread")
+ (version "1.48.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ShortRead" version))
+ (sha256
+ (base32
+ "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
+ (properties `((upstream-name . "ShortRead")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "https://bioconductor.org/packages/ShortRead")
+ (synopsis "FASTQ input and manipulation tools")
+ (description
+ "This package implements sampling, iteration, and input of FASTQ files.
+It includes functions for filtering and trimming reads, and for generating a
+quality assessment report. Data are represented as
+@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
+purposes. The package also contains legacy support for early single-end,
+ungapped alignment formats.")
+ (license license:artistic2.0)))
+
+(define-public r-systempiper
+ (package
+ (name "r-systempiper")
+ (version "1.24.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "systemPipeR" version))
+ (sha256
+ (base32
+ "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
+ (properties `((upstream-name . "systemPipeR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-assertthat" ,r-assertthat)
+ ("r-batchtools" ,r-batchtools)
+ ("r-biostrings" ,r-biostrings)
+ ("r-deseq2" ,r-deseq2)
+ ("r-dot" ,r-dot)
+ ("r-edger" ,r-edger)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-go-db" ,r-go-db)
+ ("r-gostats" ,r-gostats)
+ ("r-iranges" ,r-iranges)
+ ("r-limma" ,r-limma)
+ ("r-magrittr" ,r-magrittr)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-rjson" ,r-rjson)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rsvg" ,r-rsvg)
+ ("r-shortread" ,r-shortread)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-yaml" ,r-yaml)
+ ("r-variantannotation" ,r-variantannotation)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/tgirke/systemPipeR")
+ (synopsis "Next generation sequencing workflow and reporting environment")
+ (description
+ "This R package provides tools for building and running automated
+end-to-end analysis workflows for a wide range of @dfn{next generation
+sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
+Important features include a uniform workflow interface across different NGS
+applications, automated report generation, and support for running both R and
+command-line software, such as NGS aligners or peak/variant callers, on local
+computers or compute clusters. Efficient handling of complex sample sets and
+experimental designs is facilitated by a consistently implemented sample
+annotation infrastructure.")
+ (license license:artistic2.0)))
+
+(define-public r-variantannotation
+ (package
+ (name "r-variantannotation")
+ (version "1.36.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "VariantAnnotation" version))
+ (sha256
+ (base32
+ "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
+ (properties
+ `((upstream-name . "VariantAnnotation")))
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-dbi" ,r-dbi)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixgenerics" ,r-matrixgenerics)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/VariantAnnotation")
+ (synopsis "Package for annotation of genetic variants")
+ (description "This R package can annotate variants, compute amino acid
+coding changes and predict coding outcomes.")
+ (license license:artistic2.0)))
+
+(define-public r-xvector
+ (package
+ (name "r-xvector")
+ (version "0.30.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "XVector" version))
+ (sha256
+ (base32
+ "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq"))))
+ (properties
+ `((upstream-name . "XVector")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-system-zlib
+ (lambda _
+ (substitute* "DESCRIPTION"
+ (("zlibbioc, ") ""))
+ (substitute* "NAMESPACE"
+ (("import\\(zlibbioc\\)") ""))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/XVector")
+ (synopsis "Representation and manpulation of external sequences")
+ (description
+ "This package provides memory efficient S4 classes for storing sequences
+\"externally\" (behind an R external pointer, or on disk).")
+ (license license:artistic2.0)))
+
(define-public r-geneplotter
(package
(name "r-geneplotter")
(define-public r-diffbind
(package
(name "r-diffbind")
- (version "3.0.8")
+ (version "3.0.15")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
- "11svdfjp4faswrmzwkryzhd0ji2pl9vwsd35lvbfjgakbpxnyn8a"))))
+ "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(propagated-inputs
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.24.1")
+ (version "3.24.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
+ "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
("r-biomart" ,r-biomart)
("r-biostrings" ,r-biostrings)
("r-dbi" ,r-dbi)
+ ("r-dplyr" ,r-dplyr)
("r-ensembldb" ,r-ensembldb)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicalignments" ,r-genomicalignments)
(define-public r-matrixgenerics
(package
(name "r-matrixgenerics")
- (version "1.2.0")
+ (version "1.2.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "MatrixGenerics" version))
(sha256
(base32
- "1a3sw79185d6rld3wlrynkzcbp754a7jkracrmvn0ra964ia8zvc"))))
+ "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
(properties
`((upstream-name . "MatrixGenerics")))
(build-system r-build-system)
surface of a flowcell.")
(license license:expat)))
-;; This is a CRAN package, but it depends on packages from Bioconductor.
-(define-public r-gkmsvm
- (package
- (name "r-gkmsvm")
- (version "0.81.0")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "gkmSVM" version))
- (sha256
- (base32
- "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
- (properties `((upstream-name . "gkmSVM")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-kernlab" ,r-kernlab)
- ("r-rcpp" ,r-rcpp)
- ("r-rocr" ,r-rocr)
- ("r-seqinr" ,r-seqinr)))
- (home-page "https://cran.r-project.org/web/packages/gkmSVM")
- (synopsis "Gapped-kmer support vector machine")
- (description
- "This R package provides tools for training gapped-kmer SVM classifiers
-for DNA and protein sequences. This package supports several sequence
-kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
- (license license:gpl2+)))
-
;; This is a CRAN package, but it depends on multtest from Bioconductor.
(define-public r-mutoss
(package
(define-public r-enrichplot
(package
(name "r-enrichplot")
- (version "1.10.1")
+ (version "1.10.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "enrichplot" version))
(sha256
(base32
- "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd"))))
+ "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cowplot" ,r-cowplot)
(define-public r-clusterprofiler
(package
(name "r-clusterprofiler")
- (version "3.18.0")
+ (version "3.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "clusterProfiler" version))
(sha256
(base32
- "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9"))))
+ "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
(properties
`((upstream-name . "clusterProfiler")))
(build-system r-build-system)
(define-public r-multidataset
(package
(name "r-multidataset")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiDataSet" version))
(sha256
(base32
- "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w"))))
+ "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4"))))
(properties `((upstream-name . "MultiDataSet")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "2.4.2")
+ (version "2.4.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra"))))
+ "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
(define-public r-cytolib
(package
(name "r-cytolib")
- (version "2.2.0")
+ (version "2.2.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cytolib" version))
(sha256
(base32
- "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw"))))
+ "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
(properties `((upstream-name . "cytolib")))
(build-system r-build-system)
(arguments
(define-public r-cytoml
(package
(name "r-cytoml")
- (version "2.2.1")
+ (version "2.2.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CytoML" version))
(sha256
(base32
- "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq"))))
+ "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1"))))
(properties `((upstream-name . "CytoML")))
(build-system r-build-system)
(arguments
(string-append match "/libhdf5.a")))
#t)))))
(inputs
- `(("libxml2" ,libxml2)))
+ `(("libxml2" ,libxml2)
+ ("zlib" ,zlib)))
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
("r-bh" ,r-bh)
,@(alist-delete "r-monocle"
(package-propagated-inputs r-cicero)))))))
+(define-public r-circrnaprofiler
+ (package
+ (name "r-circrnaprofiler")
+ (version "1.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "circRNAprofiler" version))
+ (sha256
+ (base32
+ "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
+ (properties
+ `((upstream-name . "circRNAprofiler")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationhub" ,r-annotationhub)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+ ("r-deseq2" ,r-deseq2)
+ ("r-dplyr" ,r-dplyr)
+ ("r-edger" ,r-edger)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gwascat" ,r-gwascat)
+ ("r-iranges" ,r-iranges)
+ ("r-magrittr" ,r-magrittr)
+ ("r-r-utils" ,r-r-utils)
+ ("r-readr" ,r-readr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rlang" ,r-rlang)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqinr" ,r-seqinr)
+ ("r-stringi" ,r-stringi)
+ ("r-stringr" ,r-stringr)
+ ("r-universalmotif" ,r-universalmotif)))
+ (native-inputs
+ `(("r-knitr" ,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
(let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
(revision "0"))
(define-public r-gdsfmt
(package
(name "r-gdsfmt")
- (version "1.26.0")
+ (version "1.26.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gdsfmt" version))
(sha256
(base32
- "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a"))
+ "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
(modules '((guix build utils)))
;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
;; them and link with system libraries instead.
(base32
"1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
(properties
- `((upstream-name . "unifiedWMWqPCR")))
+ `((upstream-name . "unifiedWMWqPCR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-htqpcr" ,r-htqpcr)))
+ (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
+ (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
+ (description
+ "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
+data. This modified test allows for testing differential expression in qPCR
+data.")
+ (license license:gpl2+)))
+
+(define-public r-universalmotif
+ (package
+ (name "r-universalmotif")
+ (version "1.8.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "universalmotif" version))
+ (sha256
+ (base32
+ "0pmi5mp5v0srr482vlkfmkp28bywq969fvv9g5kjl5rxki963zmr"))))
+ (properties
+ `((upstream-name . "universalmotif")))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-reference-to-strip
+ (lambda _
+ (substitute* "src/Makevars"
+ (("/usr/bin/strip") (which "strip"))))))))
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
- ("r-htqpcr" ,r-htqpcr)))
- (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
- (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
- (description
- "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
-data. This modified test allows for testing differential expression in qPCR
-data.")
- (license license:gpl2+)))
+ ("r-biostrings" ,r-biostrings)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggseqlogo" ,r-ggseqlogo)
+ ("r-iranges" ,r-iranges)
+ ("r-mass" ,r-mass)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppthread" ,r-rcppthread)
+ ("r-rdpack" ,r-rdpack)
+ ("r-rlang" ,r-rlang)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://bioconductor.org/packages/universalmotif/")
+ (synopsis
+ "Specific structures importer, modifier, and exporter for R")
+ (description
+ "This package allows importing most common @dfn{specific structure}
+(motif) types into R for use by functions provided by other Bioconductor
+motif-related packages. Motifs can be exported into most major motif formats
+from various classes as defined by other Bioconductor packages. A suite of
+motif and sequence manipulation and analysis functions are included, including
+enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
+motifs, and others.")
+ (license license:gpl3)))
;; This is a CRAN package, but it depends on Bioconductor packages, so we put
;; it here.
(define-public r-chemminer
(package
(name "r-chemminer")
- (version "3.42.0")
+ (version "3.42.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChemmineR" version))
(sha256
(base32
- "14q9zhhxgkx5skj424i2rbjdbp5j8jfkxspkhnkwv5i45cvkgh19"))))
+ "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
(properties `((upstream-name . "ChemmineR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-bioassayr
(package
(name "r-bioassayr")
- (version "1.28.0")
+ (version "1.28.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bioassayR" version))
(sha256
(base32
- "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f"))))
+ "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5"))))
(properties `((upstream-name . "bioassayR")))
(build-system r-build-system)
(propagated-inputs
("r-xml" ,r-xml)))
(native-inputs
`(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/TylerBackman/bioassayR")
+ (home-page "https://github.com/girke-lab/bioassayR")
(synopsis "Cross-target analysis of small molecule bioactivity")
(description
"bioassayR is a computational tool that enables simultaneous analysis of
monograph.")
(license license:artistic2.0)))
+(define-public r-bioccheck
+ (package
+ (name "r-bioccheck")
+ (version "1.26.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocCheck" version))
+ (sha256
+ (base32
+ "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
+ (properties
+ `((upstream-name . "BiocCheck")))
+ (build-system r-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ ;; This package can be used by calling BiocCheck(<package>) from
+ ;; within R, or by running R CMD BiocCheck <package>. This phase
+ ;; makes sure the latter works. For this to work, the BiocCheck
+ ;; script must be somewhere on the PATH (not the R bin directory).
+ (add-after 'install 'install-bioccheck-subcommand
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (dest-dir (string-append out "/bin"))
+ (script-dir
+ (string-append out "/site-library/BiocCheck/script/")))
+ (mkdir-p dest-dir)
+ (symlink (string-append script-dir "/checkBadDeps.R")
+ (string-append dest-dir "/checkBadDeps.R"))
+ (symlink (string-append script-dir "/BiocCheck")
+ (string-append dest-dir "/BiocCheck")))
+ #t)))))
+ (propagated-inputs
+ `(("r-codetools" ,r-codetools)
+ ("r-graph" ,r-graph)
+ ("r-httr" ,r-httr)
+ ("r-knitr" ,r-knitr)
+ ("r-optparse" ,r-optparse)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-biocviews" ,r-biocviews)
+ ("r-stringdist" ,r-stringdist)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/BiocCheck")
+ (synopsis "Executes Bioconductor-specific package checks")
+ (description "This package contains tools to perform additional quality
+checks on R packages that are to be submitted to the Bioconductor repository.")
+ (license license:artistic2.0)))
+
(define-public r-biocgraph
(package
(name "r-biocgraph")
different graph related packages produced by Bioconductor.")
(license license:artistic2.0)))
+(define-public r-biocstyle
+ (package
+ (name "r-biocstyle")
+ (version "2.18.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocStyle" version))
+ (sha256
+ (base32
+ "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
+ (properties
+ `((upstream-name . "BiocStyle")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocmanager" ,r-biocmanager)
+ ("r-bookdown" ,r-bookdown)
+ ("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/BiocStyle")
+ (synopsis "Bioconductor formatting styles")
+ (description "This package provides standard formatting styles for
+Bioconductor PDF and HTML documents. Package vignettes illustrate use and
+functionality.")
+ (license license:artistic2.0)))
+
+(define-public r-biocviews
+ (package
+ (name "r-biocviews")
+ (version "1.58.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biocViews" version))
+ (sha256
+ (base32
+ "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
+ (properties
+ `((upstream-name . "biocViews")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-graph" ,r-graph)
+ ("r-rbgl" ,r-rbgl)
+ ("r-rcurl" ,r-rcurl)
+ ("r-xml" ,r-xml)
+ ("r-runit" ,r-runit)))
+ (home-page "https://bioconductor.org/packages/biocViews")
+ (synopsis "Bioconductor package categorization helper")
+ (description "The purpose of biocViews is to create HTML pages that
+categorize packages in a Bioconductor package repository according to keywords,
+also known as views, in a controlled vocabulary.")
+ (license license:artistic2.0)))
+
(define-public r-experimenthub
(package
(name "r-experimenthub")
access.")
(license license:artistic2.0)))
+(define-public r-grohmm
+ (package
+ (name "r-grohmm")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "groHMM" version))
+ (sha256
+ (base32
+ "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
+ (properties `((upstream-name . "groHMM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-mass" ,r-mass)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/Kraus-Lab/groHMM")
+ (synopsis "GRO-seq analysis pipeline")
+ (description
+ "This package provides a pipeline for the analysis of GRO-seq data.")
+ (license license:gpl3+)))
+
(define-public r-multiassayexperiment
(package
(name "r-multiassayexperiment")
(define-public r-preprocesscore
(package
(name "r-preprocesscore")
- (version "1.52.0")
+ (version "1.52.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "preprocessCore" version))
(sha256
(base32
- "1i5ky3bfbkrz4lgfs72fkckr8q3wq48p38mp05cjmnmh1chmdw38"))))
+ "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
(properties
`((upstream-name . "preprocessCore")))
(build-system r-build-system)
routines.")
(license license:lgpl2.0+)))
+(define-public r-s4vectors
+ (package
+ (name "r-s4vectors")
+ (version "0.28.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "S4Vectors" version))
+ (sha256
+ (base32
+ "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh"))))
+ (properties
+ `((upstream-name . "S4Vectors")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)))
+ (home-page "https://bioconductor.org/packages/S4Vectors")
+ (synopsis "S4 implementation of vectors and lists")
+ (description
+ "The S4Vectors package defines the @code{Vector} and @code{List} virtual
+classes and a set of generic functions that extend the semantic of ordinary
+vectors and lists in R. Package developers can easily implement vector-like
+or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
+In addition, a few low-level concrete subclasses of general interest (e.g.
+@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
+S4Vectors package itself.")
+ (license license:artistic2.0)))
+
;; This is a CRAN package, but it depends on preprocessorcore, which is a
;; Bioconductor package.
(define-public r-wgcna
(package
(name "r-wgcna")
- (version "1.69")
+ (version "1.70-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "WGCNA" version))
(sha256
(base32
- "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
+ "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
(properties `((upstream-name . "WGCNA")))
(build-system r-build-system)
(propagated-inputs
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "1hr149q03p09y1cjnx8av854j53041wfyq66xpsjw4mypzjf6f28"))))
+ "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(arguments
(define-public r-rhdf5lib
(package
(name "r-rhdf5lib")
- (version "1.12.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhdf5lib" version))
(sha256
(base32
- "0wia85a6dkgibsjcmpqas5068msck3h3bqpgw2x07bk189z4vay2"))
+ "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
(modules '((guix build utils)))
(snippet
'(begin
(define-public r-beachmat
(package
(name "r-beachmat")
- (version "2.6.2")
+ (version "2.6.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "beachmat" version))
(sha256
(base32
- "1yxm5andf4hsxxsmwrn5vl79707yfqkhzzajq6fvhsmaad3f97n7"))))
+ "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
matrices.")
(license license:gpl3)))
+;; This package includes files that have been taken from kentutils. Some
+;; parts of kentutils are not released under a free license, but this package
+;; only uses files that are also found in the free parts of kentutils.
+(define-public r-cner
+ (package
+ (name "r-cner")
+ (version "1.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CNEr" version))
+ (sha256
+ (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
+ (properties `((upstream-name . "CNEr")))
+ (build-system r-build-system)
+ (inputs `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-dbi" ,r-dbi)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-go-db" ,r-go-db)
+ ("r-iranges" ,r-iranges)
+ ("r-keggrest" ,r-keggrest)
+ ("r-powerlaw" ,r-powerlaw)
+ ("r-r-utils" ,r-r-utils)
+ ("r-readr" ,r-readr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xvector" ,r-xvector)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/ge11232002/CNEr")
+ (synopsis "CNE Detection and Visualization")
+ (description
+ "This package provides tools for large-scale identification and
+advanced visualization of sets of conserved noncoding elements.")
+ ;; For all files in src/ucsc "license is hereby granted for all use -
+ ;; public, private or commercial"; this includes those files that don't
+ ;; have a license header, because they are included in the free parts of
+ ;; the kentutils package.
+ (license (list license:gpl2
+ (license:non-copyleft
+ "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
+
+(define-public r-tfbstools
+ (package
+ (name "r-tfbstools")
+ (version "1.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "TFBSTools" version))
+ (sha256
+ (base32
+ "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
+ (properties `((upstream-name . "TFBSTools")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-catools" ,r-catools)
+ ("r-cner" ,r-cner)
+ ("r-dbi" ,r-dbi)
+ ("r-dirichletmultinomial" ,r-dirichletmultinomial)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqlogo" ,r-seqlogo)
+ ("r-tfmpvalue" ,r-tfmpvalue)
+ ("r-xml" ,r-xml)
+ ("r-xvector" ,r-xvector)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/ge11232002/TFBSTools")
+ (synopsis "Transcription factor binding site (TFBS) analysis")
+ (description
+ "TFBSTools is a package for the analysis and manipulation of
+transcription factor binding sites. It includes matrices conversion
+between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
+Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
+scan putative TFBS from sequence/alignment, query JASPAR database and
+provides a wrapper of de novo motif discovery software.")
+ (license license:gpl2)))
+
+(define-public r-motifmatchr
+ (package
+ (name "r-motifmatchr")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "motifmatchr" version))
+ (sha256
+ (base32
+ "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z"))))
+ (properties `((upstream-name . "motifmatchr")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-tfbstools" ,r-tfbstools)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/motifmatchr")
+ (synopsis "Fast motif matching in R")
+ (description
+ "Quickly find motif matches for many motifs and many sequences.
+This package wraps C++ code from the MOODS motif calling library.")
+ (license license:gpl3)))
+
+(define-public r-chromvar
+ (package
+ (name "r-chromvar")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "chromVAR" version))
+ (sha256
+ (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819"))))
+ (properties `((upstream-name . "chromVAR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-dt" ,r-dt)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-miniui" ,r-miniui)
+ ("r-nabor" ,r-nabor)
+ ("r-plotly" ,r-plotly)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtsne" ,r-rtsne)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shiny" ,r-shiny)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-tfbstools" ,r-tfbstools)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
+ (synopsis "Determine chromatin variation across regions")
+ (description
+ "This package @code{r-chromvar} determines variation in chromatin
+accessibility across sets of annotations or peaks. @code{r-chromvar} is
+designed primarily for single-cell or sparse chromatin accessibility data like
+single cell assay for transposase-accessible chromatin using
+sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
+sequence (@code{DNAse-seq}) experiments.")
+ (license license:expat)))
+
(define-public r-singlecellexperiment
(package
(name "r-singlecellexperiment")
(define-public r-scuttle
(package
(name "r-scuttle")
- (version "1.0.3")
+ (version "1.0.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scuttle" version))
(sha256
(base32
- "0l2r6fhyd33dllf2mc5a1pd5sawfvcin54pgh9l1nafqzg3sdv2m"))))
+ "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
(properties `((upstream-name . "scuttle")))
(build-system r-build-system)
(propagated-inputs
(define-public r-scater
(package
(name "r-scater")
- (version "1.18.3")
+ (version "1.18.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scater" version))
(sha256
(base32
- "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535"))))
+ "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
(define-public r-scran
(package
(name "r-scran")
- (version "1.18.1")
+ (version "1.18.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "1zap12rm61z2hg6ykknbif478nr7g468v8mp50bj5hqgi69ywcww"))))
+ "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
(define-public r-sparsematrixstats
(package
(name "r-sparsematrixstats")
- (version "1.2.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sparseMatrixStats" version))
(sha256
(base32
- "0d1idbda1pzhdam9m0i5rn0c6pl7gwv0v3mcrv4wi5760v9qd5qh"))))
+ "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
(properties
`((upstream-name . "sparseMatrixStats")))
(build-system r-build-system)
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
- (version "1.12.1")
+ (version "1.12.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DelayedMatrixStats" version))
(sha256
(base32
- "1cyvj6ffl10vaiip146dldc1w8if854kpz9nhi50ndhpkmdb8sa0"))))
+ "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
(properties
`((upstream-name . "DelayedMatrixStats")))
(build-system r-build-system)
"https://bioconductor.org/packages/msmsTests")
(synopsis "Differential LC-MS/MS expression tests")
(description
- "This packages provides statistical tests for label-free LC-MS/MS data
+ "This package provides statistical tests for label-free LC-MS/MS data
by spectral counts, to discover differentially expressed proteins between two
biological conditions. Three tests are available: Poisson GLM regression,
quasi-likelihood GLM regression, and the negative binomial of the edgeR
-package.The three models admit blocking factors to control for nuissance
-variables.To assure a good level of reproducibility a post-test filter is
+package. The three models admit blocking factors to control for nuisance
+variables. To assure a good level of reproducibility a post-test filter is
available, where we may set the minimum effect size considered biologicaly
relevant, and the minimum expression of the most abundant condition.")
(license license:gpl2)))
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.34.0")
+ (version "1.34.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
+ "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
the earlier snpMatrix package, allowing for uncertainty in genotypes.")
(license license:gpl3)))
+(define-public r-chromstar
+ (package
+ (name "r-chromstar")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "chromstaR" version))
+ (sha256
+ (base32
+ "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1"))))
+ (properties `((upstream-name . "chromstaR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bamsignals" ,r-bamsignals)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-chromstardata" ,r-chromstardata)
+ ("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-mvtnorm" ,r-mvtnorm)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/ataudt/chromstaR")
+ (synopsis "Chromatin state analysis for ChIP-Seq data")
+ (description
+ "This package implements functions for combinatorial and differential
+analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
+export to genome browser viewable files, and functions for enrichment
+analyses.")
+ (license license:artistic2.0)))
+
(define-public r-sushi
(package
(name "r-sushi")
HCoop / jackhill / guix / guix.git / blobdiff