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-rw-r--r--gnu/packages/bioconductor.scm615
1 files changed, 598 insertions, 17 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 37cd51d16c..7ca6788dd8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -50,21 +50,14 @@
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Celegans.UCSC.ce6_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
+ version 'annotation))
(sha256
(base32
"0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
(properties
`((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
(build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
@@ -817,6 +810,28 @@ annotations.")
Disease Ontology.")
(license license:artistic2.0)))
+(define-public r-pfam-db
+ (package
+ (name "r-pfam-db")
+ (version "3.8.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "PFAM.db" version 'annotation))
+ (sha256
+ (base32
+ "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
+ (properties `((upstream-name . "PFAM.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://bioconductor.org/packages/PFAM.db")
+ (synopsis "Set of protein ID mappings for PFAM")
+ (description
+ "This package provides a set of protein ID mappings for PFAM, assembled
+using data from public repositories.")
+ (license license:artistic2.0)))
+
;;; Experiment data
@@ -942,6 +957,29 @@ jointly normalized data that are available here. The data are presented in
the form of an @code{exprSet} object.")
(license license:artistic2.0)))
+(define-public r-affydata
+ (package
+ (name "r-affydata")
+ (version "1.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "affydata" version 'experiment))
+ (sha256
+ (base32
+ "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
+ (properties `((upstream-name . "affydata")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)))
+ (home-page "https://bioconductor.org/packages/affydata/")
+ (synopsis "Affymetrix data for demonstration purposes")
+ (description
+ "This package provides example datasets that represent 'real world
+examples' of Affymetrix data, unlike the artificial examples included in the
+package @code{affy}.")
+ (license license:gpl2+)))
+
;;; Packages
@@ -965,6 +1003,147 @@ the form of an @code{exprSet} object.")
packages.")
(license license:artistic2.0)))
+(define-public r-affycomp
+ (package
+ (name "r-affycomp")
+ (version "1.60.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "affycomp" version))
+ (sha256
+ (base32
+ "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n"))))
+ (properties `((upstream-name . "affycomp")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-biobase" ,r-biobase)))
+ (home-page "https://bioconductor.org/packages/affycomp/")
+ (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
+ (description
+ "The package contains functions that can be used to compare expression
+measures for Affymetrix Oligonucleotide Arrays.")
+ (license license:gpl2+)))
+
+(define-public r-affycompatible
+ (package
+ (name "r-affycompatible")
+ (version "1.44.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AffyCompatible" version))
+ (sha256
+ (base32
+ "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs"))))
+ (properties
+ `((upstream-name . "AffyCompatible")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-rcurl" ,r-rcurl)
+ ("r-xml" ,r-xml)))
+ (home-page "https://bioconductor.org/packages/AffyCompatible/")
+ (synopsis "Work with Affymetrix GeneChip files")
+ (description
+ "This package provides an interface to Affymetrix chip annotation and
+sample attribute files. The package allows an easy way for users to download
+and manage local data bases of Affynmetrix NetAffx annotation files. It also
+provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
+Command Console} (AGCC)-compatible sample annotation files.")
+ (license license:artistic2.0)))
+
+(define-public r-affycontam
+ (package
+ (name "r-affycontam")
+ (version "1.42.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "affyContam" version))
+ (sha256
+ (base32
+ "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp"))))
+ (properties `((upstream-name . "affyContam")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-affydata" ,r-affydata)
+ ("r-biobase" ,r-biobase)))
+ (home-page "https://bioconductor.org/packages/affyContam/")
+ (synopsis "Structured corruption of Affymetrix CEL file data")
+ (description
+ "Microarray quality assessment is a major concern of microarray analysts.
+This package provides some simple approaches to in silico creation of quality
+problems in CEL-level data to help evaluate performance of quality metrics.")
+ (license license:artistic2.0)))
+
+(define-public r-affycoretools
+ (package
+ (name "r-affycoretools")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "affycoretools" version))
+ (sha256
+ (base32
+ "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s"))))
+ (properties `((upstream-name . "affycoretools")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-dbi" ,r-dbi)
+ ("r-edger" ,r-edger)
+ ("r-gcrma" ,r-gcrma)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gostats" ,r-gostats)
+ ("r-gplots" ,r-gplots)
+ ("r-hwriter" ,r-hwriter)
+ ("r-lattice" ,r-lattice)
+ ("r-limma" ,r-limma)
+ ("r-oligoclasses" ,r-oligoclasses)
+ ("r-reportingtools" ,r-reportingtools)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xtable" ,r-xtable)))
+ (home-page "https://bioconductor.org/packages/affycoretools/")
+ (synopsis "Functions for analyses with Affymetrix GeneChips")
+ (description
+ "This package provides various wrapper functions that have been written
+to streamline the more common analyses that a Biostatistician might see.")
+ (license license:artistic2.0)))
+
+(define-public r-affxparser
+ (package
+ (name "r-affxparser")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "affxparser" version))
+ (sha256
+ (base32
+ "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33"))))
+ (properties `((upstream-name . "affxparser")))
+ (build-system r-build-system)
+ (home-page "https://github.com/HenrikBengtsson/affxparser")
+ (synopsis "Affymetrix File Parsing SDK")
+ (description
+ "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
+BAR). It provides methods for fast and memory efficient parsing of Affymetrix
+files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
+are supported. Currently, there are methods for reading @dfn{chip definition
+file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
+either in full or in part. For example, probe signals from a few probesets
+can be extracted very quickly from a set of CEL files into a convenient list
+structure.")
+ ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
+ ;; under LGPLv2+.
+ (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
+
(define-public r-annotate
(package
(name "r-annotate")
@@ -1013,14 +1192,14 @@ the Human Protein Atlas project.")
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.16.2")
+ (version "1.16.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q"))))
+ "0xzk057h6nkr3rvd412prxgnkpq625b90laj1kwb0i5q8j5ch760"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
@@ -1039,6 +1218,54 @@ customizable permutation tests to assess the association between genomic
region sets and other genomic features.")
(license license:artistic2.0)))
+(define-public r-reportingtools
+ (package
+ (name "r-reportingtools")
+ (version "2.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ReportingTools" version))
+ (sha256
+ (base32
+ "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc"))))
+ (properties
+ `((upstream-name . "ReportingTools")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-category" ,r-category)
+ ("r-deseq2" ,r-deseq2)
+ ("r-edger" ,r-edger)
+ ("r-ggbio" ,r-ggbio)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gostats" ,r-gostats)
+ ("r-gseabase" ,r-gseabase)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-knitr" ,r-knitr)
+ ("r-lattice" ,r-lattice)
+ ("r-limma" ,r-limma)
+ ("r-pfam-db" ,r-pfam-db)
+ ("r-r-utils" ,r-r-utils)
+ ("r-xml" ,r-xml)))
+ (home-page "https://bioconductor.org/packages/ReportingTools/")
+ (synopsis "Tools for making reports in various formats")
+ (description
+ "The ReportingTools package enables users to easily display reports of
+analysis results generated from sources such as microarray and sequencing
+data. The package allows users to create HTML pages that may be viewed on a
+web browser, or in other formats. Users can generate tables with sortable and
+filterable columns, make and display plots, and link table entries to other
+data sources such as NCBI or larger plots within the HTML page. Using the
+package, users can also produce a table of contents page to link various
+reports together for a particular project that can be viewed in a web
+browser.")
+ (license license:artistic2.0)))
+
(define-public r-geneplotter
(package
(name "r-geneplotter")
@@ -1064,6 +1291,75 @@ region sets and other genomic features.")
"This package provides functions for plotting genomic data.")
(license license:artistic2.0)))
+(define-public r-oligoclasses
+ (package
+ (name "r-oligoclasses")
+ (version "1.46.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "oligoClasses" version))
+ (sha256
+ (base32
+ "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72"))))
+ (properties `((upstream-name . "oligoClasses")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affyio" ,r-affyio)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-biostrings" ,r-biostrings)
+ ("r-dbi" ,r-dbi)
+ ("r-ff" ,r-ff)
+ ("r-foreach" ,r-foreach)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/oligoClasses/")
+ (synopsis "Classes for high-throughput arrays")
+ (description
+ "This package contains class definitions, validity checks, and
+initialization methods for classes used by the @code{oligo} and @code{crlmm}
+packages.")
+ (license license:gpl2+)))
+
+(define-public r-oligo
+ (package
+ (name "r-oligo")
+ (version "1.48.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "oligo" version))
+ (sha256
+ (base32
+ "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df"))))
+ (properties `((upstream-name . "oligo")))
+ (build-system r-build-system)
+ (inputs `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-affxparser" ,r-affxparser)
+ ("r-affyio" ,r-affyio)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-dbi" ,r-dbi)
+ ("r-ff" ,r-ff)
+ ("r-oligoclasses" ,r-oligoclasses)
+ ("r-preprocesscore" ,r-preprocesscore)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (home-page "https://bioconductor.org/packages/oligo/")
+ (synopsis "Preprocessing tools for oligonucleotide arrays")
+ (description
+ "This package provides a package to analyze oligonucleotide
+arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
+Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
+ (license license:lgpl2.0+)))
+
(define-public r-qvalue
(package
(name "r-qvalue")
@@ -3895,14 +4191,14 @@ analysis.")
(define-public r-gtrellis
(package
(name "r-gtrellis")
- (version "1.16.0")
+ (version "1.16.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gtrellis" version))
(sha256
(base32
- "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y"))))
+ "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix"))))
(build-system r-build-system)
(propagated-inputs
`(("r-circlize" ,r-circlize)
@@ -4888,14 +5184,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "1.34.6")
+ (version "1.34.7")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550"))))
+ "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -5047,14 +5343,14 @@ self-organizing map clustering and minimal spanning trees.")
(define-public r-mixomics
(package
(name "r-mixomics")
- (version "6.8.2")
+ (version "6.8.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
- "0issfrhsgc102sr33q9v6w6jrrd32plig7szd1nm0n4r3yn4y2fc"))))
+ "0lw4c9lxcm83xrvl4y120i1z710qjbdqginhrw738azpr1f82hcg"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
@@ -5466,3 +5762,288 @@ with multiple R processes supported by the package @code{parallel}.")
"This package provides methods for working with Illumina arrays using the
@code{gdsfmt} package.")
(license license:gpl3)))
+
+(define-public r-seqbias
+ (package
+ (name "r-seqbias")
+ (version "1.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "seqbias" version))
+ (sha256
+ (base32
+ "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw"))))
+ (properties `((upstream-name . "seqbias")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-rhtslib" ,r-rhtslib)))
+ (inputs
+ `(("zlib" ,zlib))) ; This comes from rhtslib.
+ (home-page "https://bioconductor.org/packages/seqbias/")
+ (synopsis "Estimation of per-position bias in high-throughput sequencing data")
+ (description
+ "This package implements a model of per-position sequencing bias in
+high-throughput sequencing data using a simple Bayesian network, the structure
+and parameters of which are trained on a set of aligned reads and a reference
+genome sequence.")
+ (license license:lgpl3)))
+
+(define-public r-reqon
+ (package
+ (name "r-reqon")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ReQON" version))
+ (sha256
+ (base32
+ "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a"))))
+ (properties `((upstream-name . "ReQON")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rjava" ,r-rjava)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-seqbias" ,r-seqbias)))
+ (home-page "https://bioconductor.org/packages/ReQON/")
+ (synopsis "Recalibrating quality of nucleotides")
+ (description
+ "This package provides an implementation of an algorithm for
+recalibrating the base quality scores for aligned sequencing data in BAM
+format.")
+ (license license:gpl2)))
+
+(define-public r-wavcluster
+ (package
+ (name "r-wavcluster")
+ (version "2.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "wavClusteR" version))
+ (sha256
+ (base32
+ "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2"))))
+ (properties `((upstream-name . "wavClusteR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-foreach" ,r-foreach)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-hmisc" ,r-hmisc)
+ ("r-iranges" ,r-iranges)
+ ("r-mclust" ,r-mclust)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqinr" ,r-seqinr)
+ ("r-stringr" ,r-stringr)
+ ("r-wmtsa" ,r-wmtsa)))
+ (home-page "https://bioconductor.org/packages/wavClusteR/")
+ (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
+ (description
+ "This package provides an integrated pipeline for the analysis of
+PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
+sequencing errors, SNPs and additional non-experimental sources by a non-
+parametric mixture model. The protein binding sites (clusters) are then
+resolved at high resolution and cluster statistics are estimated using a
+rigorous Bayesian framework. Post-processing of the results, data export for
+UCSC genome browser visualization and motif search analysis are provided. In
+addition, the package allows to integrate RNA-Seq data to estimate the False
+Discovery Rate of cluster detection. Key functions support parallel multicore
+computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
+be applied to the analysis of other NGS data obtained from experimental
+procedures that induce nucleotide substitutions (e.g. BisSeq).")
+ (license license:gpl2)))
+
+(define-public r-timeseriesexperiment
+ (package
+ (name "r-timeseriesexperiment")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "TimeSeriesExperiment" version))
+ (sha256
+ (base32
+ "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y"))))
+ (properties
+ `((upstream-name . "TimeSeriesExperiment")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-deseq2" ,r-deseq2)
+ ("r-dplyr" ,r-dplyr)
+ ("r-dynamictreecut" ,r-dynamictreecut)
+ ("r-edger" ,r-edger)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-hmisc" ,r-hmisc)
+ ("r-limma" ,r-limma)
+ ("r-magrittr" ,r-magrittr)
+ ("r-proxy" ,r-proxy)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-vegan" ,r-vegan)
+ ("r-viridis" ,r-viridis)))
+ (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
+ (synopsis "Analysis for short time-series data")
+ (description
+ "This package is a visualization and analysis toolbox for short time
+course data which includes dimensionality reduction, clustering, two-sample
+differential expression testing and gene ranking techniques. The package also
+provides methods for retrieving enriched pathways.")
+ (license license:lgpl3+)))
+
+(define-public r-variantfiltering
+ (package
+ (name "r-variantfiltering")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "VariantFiltering" version))
+ (sha256
+ (base32
+ "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17"))))
+ (properties
+ `((upstream-name . "VariantFiltering")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("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-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-genomicscores" ,r-genomicscores)
+ ("r-graph" ,r-graph)
+ ("r-gviz" ,r-gviz)
+ ("r-iranges" ,r-iranges)
+ ("r-rbgl" ,r-rbgl)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shiny" ,r-shiny)
+ ("r-shinyjs" ,r-shinyjs)
+ ("r-shinythemes" ,r-shinythemes)
+ ("r-shinytree" ,r-shinytree)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://github.com/rcastelo/VariantFiltering")
+ (synopsis "Filtering of coding and non-coding genetic variants")
+ (description
+ "Filter genetic variants using different criteria such as inheritance
+model, amino acid change consequence, minor allele frequencies across human
+populations, splice site strength, conservation, etc.")
+ (license license:artistic2.0)))
+
+(define-public r-genomegraphs
+ (package
+ (name "r-genomegraphs")
+ (version "1.44.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomeGraphs" version))
+ (sha256
+ (base32
+ "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd"))))
+ (properties `((upstream-name . "GenomeGraphs")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biomart" ,r-biomart)))
+ (home-page "https://bioconductor.org/packages/GenomeGraphs/")
+ (synopsis "Plotting genomic information from Ensembl")
+ (description
+ "Genomic data analyses requires integrated visualization of known genomic
+information and new experimental data. GenomeGraphs uses the biomaRt package
+to perform live annotation queries to Ensembl and translates this to e.g.
+gene/transcript structures in viewports of the grid graphics package. This
+results in genomic information plotted together with your data. Another
+strength of GenomeGraphs is to plot different data types such as array CGH,
+gene expression, sequencing and other data, together in one plot using the
+same genome coordinate system.")
+ (license license:artistic2.0)))
+
+(define-public r-wavetiling
+ (package
+ (name "r-wavetiling")
+ (version "1.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "waveTiling" version))
+ (sha256
+ (base32
+ "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir"))))
+ (properties `((upstream-name . "waveTiling")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-biobase" ,r-biobase)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomegraphs" ,r-genomegraphs)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-oligo" ,r-oligo)
+ ("r-oligoclasses" ,r-oligoclasses)
+ ("r-preprocesscore" ,r-preprocesscore)
+ ("r-waveslim" ,r-waveslim)))
+ (home-page "https://r-forge.r-project.org/projects/wavetiling/")
+ (synopsis "Wavelet-based models for tiling array transcriptome analysis")
+ (description
+ "This package is designed to conduct transcriptome analysis for tiling
+arrays based on fast wavelet-based functional models.")
+ (license license:gpl2+)))
+
+(define-public r-variancepartition
+ (package
+ (name "r-variancepartition")
+ (version "1.14.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "variancePartition" version))
+ (sha256
+ (base32
+ "1ycapwb2mq57xibrzzjz9zwxqz4nwz9f3n5gskhlr5vcs7irkjd6"))))
+ (properties
+ `((upstream-name . "variancePartition")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-colorramps" ,r-colorramps)
+ ("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gplots" ,r-gplots)
+ ("r-iterators" ,r-iterators)
+ ("r-limma" ,r-limma)
+ ("r-lme4" ,r-lme4)
+ ("r-lmertest" ,r-lmertest)
+ ("r-mass" ,r-mass)
+ ("r-pbkrtest" ,r-pbkrtest)
+ ("r-progress" ,r-progress)
+ ("r-reshape2" ,r-reshape2)
+ ("r-scales" ,r-scales)))
+ (home-page "https://bioconductor.org/packages/variancePartition/")
+ (synopsis "Analyze variation in gene expression experiments")
+ (description
+ "This is a package providing tools to quantify and interpret multiple
+sources of biological and technical variation in gene expression experiments.
+It uses a linear mixed model to quantify variation in gene expression
+attributable to individual, tissue, time point, or technical variables. The
+package includes dream differential expression analysis for repeated
+measures.")
+ (license license:gpl2+)))
generated by cgit v1.2.3 (git 2.25.4) at 2024-06-30 15:53:37 +0000