;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
+ #:use-module (guix git-download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
- #:use-module (gnu packages haskell)
+ #:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages image)
#:use-module (gnu packages maths)
#:use-module (gnu packages netpbm)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
- #:use-module (gnu packages web))
+ #:use-module (gnu packages web)
+ #:use-module (srfi srfi-1))
\f
;;; Annotations
(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
by UCSC (hg19, February 2009) and stored in Biostrings objects.")
(license license:artistic2.0)))
+(define-public r-ensdb-hsapiens-v75
+ (package
+ (name "r-ensdb-hsapiens-v75")
+ (version "2.99.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
+ (sha256
+ (base32
+ "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
+ (properties
+ `((upstream-name . "EnsDb.Hsapiens.v75")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ensembldb" ,r-ensembldb)))
+ (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
+ (synopsis "Ensembl based annotation package")
+ (description
+ "This package exposes an annotation database generated from Ensembl.")
+ (license license:artistic2.0)))
+
(define-public r-genelendatabase
(package
(name "r-genelendatabase")
based on the knownGene track.")
(license license:artistic2.0)))
+(define-public r-txdb-celegans-ucsc-ce6-ensgene
+ (package
+ (name "r-txdb-celegans-ucsc-ce6-ensgene")
+ (version "3.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
+ version 'annotation))
+ (sha256
+ (base32
+ "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
+ (properties
+ `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-genomicfeatures" ,r-genomicfeatures)))
+ (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
+ (synopsis "Annotation package for C elegans TxDb objects")
+ (description
+ "This package exposes a C elegans annotation database generated from UCSC
+by exposing these as TxDb objects.")
+ (license license:artistic2.0)))
+
(define-public r-fdb-infiniummethylation-hg19
(package
(name "r-fdb-infiniummethylation-hg19")
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)))
+
+(define-public r-phastcons100way-ucsc-hg19
+ (package
+ (name "r-phastcons100way-ucsc-hg19")
+ (version "3.7.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
+ version 'annotation))
+ (sha256
+ (base32
+ "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
+ (properties
+ `((upstream-name . "phastCons100way.UCSC.hg19")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-genomicscores" ,r-genomicscores)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
+ (synopsis "UCSC phastCons conservation scores for hg19")
+ (description
+ "This package provides UCSC phastCons conservation scores for the human
+genome (hg19) calculated from multiple alignments with other 99 vertebrate
+species.")
+ (license license:artistic2.0)))
+
\f
;;; Experiment data
resulting in a complete gene expression profile for each cell.")
(license license:artistic2.0)))
+(define-public r-all
+ (package
+ (name "r-all")
+ (version "1.26.0")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/experiment/" instead of "bioc/".
+ (uri (string-append "https://www.bioconductor.org/packages/"
+ "release/data/experiment/src/contrib/"
+ "ALL_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
+ (properties `((upstream-name . "ALL")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)))
+ (home-page "https://bioconductor.org/packages/ALL")
+ (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
+ (description
+ "The data consist of microarrays from 128 different individuals with
+@dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
+are available. The data have been normalized (using rma) and it is the
+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+)))
+
\f
;;; Packages
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")
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.16.2")
+ (version "1.16.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q"))))
+ "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
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")
"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")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.18.1")
+ (version "3.18.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
+ "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
+ "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
qPCR data, but could be used with other types as well.")
(license license:artistic2.0)))
-(define-public r-noiseq
+(define-public r-monocle3
(package
- (name "r-noiseq")
- (version "2.28.0")
+ (name "r-monocle3")
+ (version "0.1.2")
(source
(origin
- (method url-fetch)
- (uri (bioconductor-uri "NOISeq" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cole-trapnell-lab/monocle3.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
- (properties `((upstream-name . "NOISeq")))
+ "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
- ("r-matrix" ,r-matrix)))
- (home-page "https://bioconductor.org/packages/NOISeq")
- (synopsis "Exploratory analysis and differential expression for RNA-seq data")
- (description
- "This package provides tools to support the analysis of RNA-seq
-expression data or other similar kind of data. It provides exploratory plots
-to evaluate saturation, count distribution, expression per chromosome, type of
-detected features, features length, etc. It also supports the analysis of
-differential expression between two experimental conditions with no parametric
-assumptions.")
- (license license:artistic2.0)))
-
-(define-public r-scdd
- (package
- (name "r-scdd")
- (version "1.8.0")
- (source
- (origin
- (method url-fetch)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-grr" ,r-grr)
+ ("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-limma" ,r-limma)
+ ("r-lmtest" ,r-lmtest)
+ ("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-matrix-utils" ,r-matrix-utils)
+ ("r-pbapply" ,r-pbapply)
+ ("r-pbmcapply" ,r-pbmcapply)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-plotly" ,r-plotly)
+ ("r-pryr" ,r-pryr)
+ ("r-proxy" ,r-proxy)
+ ("r-pscl" ,r-pscl)
+ ("r-purrr" ,r-purrr)
+ ("r-rann" ,r-rann)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppparallel" ,r-rcppparallel)
+ ("r-reshape2" ,r-reshape2)
+ ("r-reticulate" ,r-reticulate)
+ ("r-rhpcblasctl" ,r-rhpcblasctl)
+ ("r-rtsne" ,r-rtsne)
+ ("r-shiny" ,r-shiny)
+ ("r-slam" ,r-slam)
+ ("r-spdep" ,r-spdep)
+ ("r-speedglm" ,r-speedglm)
+ ("r-stringr" ,r-stringr)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-uwot" ,r-uwot)
+ ("r-viridis" ,r-viridis)))
+ (home-page "https://github.com/cole-trapnell-lab/monocle3")
+ (synopsis "Analysis toolkit for single-cell RNA-Seq data")
+ (description
+ "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
+ (license license:expat)))
+
+(define-public r-noiseq
+ (package
+ (name "r-noiseq")
+ (version "2.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "NOISeq" version))
+ (sha256
+ (base32
+ "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
+ (properties `((upstream-name . "NOISeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-matrix" ,r-matrix)))
+ (home-page "https://bioconductor.org/packages/NOISeq")
+ (synopsis "Exploratory analysis and differential expression for RNA-seq data")
+ (description
+ "This package provides tools to support the analysis of RNA-seq
+expression data or other similar kind of data. It provides exploratory plots
+to evaluate saturation, count distribution, expression per chromosome, type of
+detected features, features length, etc. It also supports the analysis of
+differential expression between two experimental conditions with no parametric
+assumptions.")
+ (license license:artistic2.0)))
+
+(define-public r-scdd
+ (package
+ (name "r-scdd")
+ (version "1.8.0")
+ (source
+ (origin
+ (method url-fetch)
(uri (bioconductor-uri "scDD" version))
(sha256
(base32
(define-public r-fgsea
(package
(name "r-fgsea")
- (version "1.10.0")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fgsea" version))
(sha256
(base32
- "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c"))))
+ "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
(define-public r-mlinterfaces
(package
(name "r-mlinterfaces")
- (version "1.64.0")
+ (version "1.64.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MLInterfaces" version))
(sha256
(base32
- "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
+ "1c1hciwy37zpr5bzdjj2xxx2r4jdfmr5w0zmg010lm2985z41gqh"))))
(properties `((upstream-name . "MLInterfaces")))
(build-system r-build-system)
(propagated-inputs
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
- (version "1.8.1")
+ (version "1.8.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
- "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69"))))
+ "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
(define-public r-abaenrichment
(package
(name "r-abaenrichment")
- (version "1.14.0")
+ (version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ABAEnrichment" version))
(sha256
(base32
- "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
+ "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
(properties `((upstream-name . "ABAEnrichment")))
(build-system r-build-system)
(propagated-inputs
(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)
(define-public r-xcms
(package
(name "r-xcms")
- (version "3.6.1")
+ (version "3.6.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "xcms" version))
(sha256
(base32
- "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
+ "0icww3f1kahyk96mc07yhsbyiranzm2614n509as09jf8bdhq23v"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "1.34.4")
+ (version "1.34.7")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "1230p8nsakifmpsqfiaj8rpm7npa8ab903mfjmayfa71n6yzvcbs"))))
+ "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
gene fusion discovery. It can be applied to all major sequencing techologies
and to both short and long sequence reads.")
(license license:gpl3)))
+
+(define-public r-flowutils
+ (package
+ (name "r-flowutils")
+ (version "1.48.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "flowUtils" version))
+ (sha256
+ (base32
+ "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
+ (properties `((upstream-name . "flowUtils")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-corpcor" ,r-corpcor)
+ ("r-flowcore" ,r-flowcore)
+ ("r-graph" ,r-graph)
+ ("r-runit" ,r-runit)
+ ("r-xml" ,r-xml)))
+ (home-page "https://github.com/jspidlen/flowUtils")
+ (synopsis "Utilities for flow cytometry")
+ (description
+ "This package provides utilities for flow cytometry data.")
+ (license license:artistic2.0)))
+
+(define-public r-consensusclusterplus
+ (package
+ (name "r-consensusclusterplus")
+ (version "1.48.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ConsensusClusterPlus" version))
+ (sha256
+ (base32
+ "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
+ (properties
+ `((upstream-name . "ConsensusClusterPlus")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-all" ,r-all)
+ ("r-biobase" ,r-biobase)
+ ("r-cluster" ,r-cluster)))
+ (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
+ (synopsis "Clustering algorithm")
+ (description
+ "This package provides an implementation of an algorithm for determining
+cluster count and membership by stability evidence in unsupervised analysis.")
+ (license license:gpl2)))
+
+(define-public r-flowcore
+ (package
+ (name "r-flowcore")
+ (version "1.50.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "flowCore" version))
+ (sha256
+ (base32
+ "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
+ (properties `((upstream-name . "flowCore")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-corpcor" ,r-corpcor)
+ ("r-graph" ,r-graph)
+ ("r-mass" ,r-mass)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rrcov" ,r-rrcov)))
+ (home-page "https://bioconductor.org/packages/flowCore")
+ (synopsis "Basic structures for flow cytometry data")
+ (description
+ "This package provides S4 data structures and basic functions to deal
+with flow cytometry data.")
+ (license license:artistic2.0)))
+
+(define-public r-flowmeans
+ (package
+ (name "r-flowmeans")
+ (version "1.44.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "flowMeans" version))
+ (sha256
+ (base32
+ "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
+ (properties `((upstream-name . "flowMeans")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-feature" ,r-feature)
+ ("r-flowcore" ,r-flowcore)
+ ("r-rrcov" ,r-rrcov)))
+ (home-page "https://bioconductor.org/packages/flowMeans")
+ (synopsis "Non-parametric flow cytometry data gating")
+ (description
+ "This package provides tools to identify cell populations in Flow
+Cytometry data using non-parametric clustering and segmented-regression-based
+change point detection.")
+ (license license:artistic2.0)))
+
+(define-public r-flowsom
+ (package
+ (name "r-flowsom")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "FlowSOM" version))
+ (sha256
+ (base32
+ "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
+ (properties `((upstream-name . "FlowSOM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-consensusclusterplus" ,r-consensusclusterplus)
+ ("r-flowcore" ,r-flowcore)
+ ("r-flowutils" ,r-flowutils)
+ ("r-igraph" ,r-igraph)
+ ("r-tsne" ,r-tsne)
+ ("r-xml" ,r-xml)))
+ (home-page "https://bioconductor.org/packages/FlowSOM/")
+ (synopsis "Visualize and interpret cytometry data")
+ (description
+ "FlowSOM offers visualization options for cytometry data, by using
+self-organizing map clustering and minimal spanning trees.")
+ (license license:gpl2+)))
+
+(define-public r-mixomics
+ (package
+ (name "r-mixomics")
+ (version "6.8.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "mixOmics" version))
+ (sha256
+ (base32
+ "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7"))))
+ (properties `((upstream-name . "mixOmics")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-corpcor" ,r-corpcor)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ellipse" ,r-ellipse)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-igraph" ,r-igraph)
+ ("r-lattice" ,r-lattice)
+ ("r-mass" ,r-mass)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rarpack" ,r-rarpack)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-reshape2" ,r-reshape2)
+ ("r-tidyr" ,r-tidyr)))
+ (home-page "http://www.mixOmics.org")
+ (synopsis "Multivariate methods for exploration of biological datasets")
+ (description
+ "mixOmics offers a wide range of multivariate methods for the exploration
+and integration of biological datasets with a particular focus on variable
+selection. The package proposes several sparse multivariate models we have
+developed to identify the key variables that are highly correlated, and/or
+explain the biological outcome of interest. The data that can be analysed
+with mixOmics may come from high throughput sequencing technologies, such as
+omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
+also beyond the realm of omics (e.g. spectral imaging). The methods
+implemented in mixOmics can also handle missing values without having to
+delete entire rows with missing data.")
+ (license license:gpl2+)))
+
+(define-public r-depecher
+ (package
+ (name "r-depecher")
+ (version "1.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DepecheR" version))
+ (sha256
+ (base32
+ "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
+ (properties `((upstream-name . "DepecheR")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-syntax-error
+ (lambda _
+ (substitute* "src/Makevars"
+ ((" & ") " && "))
+ #t)))))
+ (propagated-inputs
+ `(("r-beanplot" ,r-beanplot)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-dosnow" ,r-dosnow)
+ ("r-dplyr" ,r-dplyr)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gplots" ,r-gplots)
+ ("r-mass" ,r-mass)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-mixomics" ,r-mixomics)
+ ("r-moments" ,r-moments)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-reshape2" ,r-reshape2)
+ ("r-viridis" ,r-viridis)))
+ (home-page "https://bioconductor.org/packages/DepecheR/")
+ (synopsis "Identify traits of clusters in high-dimensional entities")
+ (description
+ "The purpose of this package is to identify traits in a dataset that can
+separate groups. This is done on two levels. First, clustering is performed,
+using an implementation of sparse K-means. Secondly, the generated clusters
+are used to predict outcomes of groups of individuals based on their
+distribution of observations in the different clusters. As certain clusters
+with separating information will be identified, and these clusters are defined
+by a sparse number of variables, this method can reduce the complexity of
+data, to only emphasize the data that actually matters.")
+ (license license:expat)))
+
+(define-public r-rcistarget
+ (package
+ (name "r-rcistarget")
+ (version "1.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RcisTarget" version))
+ (sha256
+ (base32
+ "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
+ (properties `((upstream-name . "RcisTarget")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-aucell" ,r-aucell)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-data-table" ,r-data-table)
+ ("r-feather" ,r-feather)
+ ("r-gseabase" ,r-gseabase)
+ ("r-r-utils" ,r-r-utils)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://aertslab.org/#scenic")
+ (synopsis "Identify transcription factor binding motifs enriched on a gene list")
+ (description
+ "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
+over-represented on a gene list. In a first step, RcisTarget selects DNA
+motifs that are significantly over-represented in the surroundings of the
+@dfn{transcription start site} (TSS) of the genes in the gene-set. This is
+achieved by using a database that contains genome-wide cross-species rankings
+for each motif. The motifs that are then annotated to TFs and those that have
+a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
+each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
+genes in the gene-set that are ranked above the leading edge).")
+ (license license:gpl3)))
+
+(define-public r-cicero
+ (package
+ (name "r-cicero")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "cicero" version))
+ (sha256
+ (base32
+ "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-assertthat" ,r-assertthat)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
+ ("r-fnn" ,r-fnn)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-glasso" ,r-glasso)
+ ("r-gviz" ,r-gviz)
+ ("r-igraph" ,r-igraph)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-monocle" ,r-monocle)
+ ("r-plyr" ,r-plyr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-vgam" ,r-vgam)))
+ (home-page "https://bioconductor.org/packages/cicero/")
+ (synopsis "Predict cis-co-accessibility from single-cell data")
+ (description
+ "Cicero computes putative cis-regulatory maps from single-cell chromatin
+accessibility data. It also extends the monocle package for use in chromatin
+accessibility data.")
+ (license license:expat)))
+
+;; This is the latest commit on the "monocle3" branch.
+(define-public r-cicero-monocle3
+ (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
+ (revision "1"))
+ (package (inherit r-cicero)
+ (name "r-cicero-monocle3")
+ (version (git-version "1.3.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cole-trapnell-lab/cicero-release.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
+ (propagated-inputs
+ `(("r-monocle3" ,r-monocle3)
+ ,@(alist-delete "r-monocle"
+ (package-propagated-inputs r-cicero)))))))
+
+(define-public r-cistopic
+ (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
+ (revision "0"))
+ (package
+ (name "r-cistopic")
+ (version (git-version "0.2.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/aertslab/cisTopic.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-aucell" ,r-aucell)
+ ("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
+ ("r-dosnow" ,r-dosnow)
+ ("r-dt" ,r-dt)
+ ("r-feather" ,r-feather)
+ ("r-fitdistrplus" ,r-fitdistrplus)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-lda" ,r-lda)
+ ("r-matrix" ,r-matrix)
+ ("r-plyr" ,r-plyr)
+ ("r-rcistarget" ,r-rcistarget)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/aertslab/cisTopic")
+ (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
+ (description
+ "The sparse nature of single cell epigenomics data can be overruled using
+probabilistic modelling methods such as @dfn{Latent Dirichlet
+Allocation} (LDA). This package allows the probabilistic modelling of
+cis-regulatory topics (cisTopics) from single cell epigenomics data, and
+includes functionalities to identify cell states based on the contribution of
+cisTopics and explore the nature and regulatory proteins driving them.")
+ (license license:gpl3))))
+
+(define-public r-genie3
+ (package
+ (name "r-genie3")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GENIE3" version))
+ (sha256
+ (base32
+ "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
+ (properties `((upstream-name . "GENIE3")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-reshape2" ,r-reshape2)))
+ (home-page "https://bioconductor.org/packages/GENIE3")
+ (synopsis "Gene network inference with ensemble of trees")
+ (description
+ "This package implements the GENIE3 algorithm for inferring gene
+regulatory networks from expression data.")
+ (license license:gpl2+)))
+
+(define-public r-roc
+ (package
+ (name "r-roc")
+ (version "1.60.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ROC" version))
+ (sha256
+ (base32
+ "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
+ (properties `((upstream-name . "ROC")))
+ (build-system r-build-system)
+ (home-page "https://www.bioconductor.org/packages/ROC/")
+ (synopsis "Utilities for ROC curves")
+ (description
+ "This package provides utilities for @dfn{Receiver Operating
+Characteristic} (ROC) curves, with a focus on micro arrays.")
+ (license license:artistic2.0)))
+
+(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
+ (package
+ (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
+ (version "0.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri
+ "IlluminaHumanMethylation450kanno.ilmn12.hg19"
+ version 'annotation))
+ (sha256
+ (base32
+ "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
+ (properties
+ `((upstream-name
+ . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-minfi" ,r-minfi)))
+ (home-page
+ "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
+ (synopsis "Annotation for Illumina's 450k methylation arrays")
+ (description
+ "This package provides manifests and annotation for Illumina's 450k array
+data.")
+ (license license:artistic2.0)))
+
+(define-public r-watermelon
+ (package
+ (name "r-watermelon")
+ (version "1.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "wateRmelon" version))
+ (sha256
+ (base32
+ "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
+ (properties `((upstream-name . "wateRmelon")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
+ ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
+ ("r-illuminaio" ,r-illuminaio)
+ ("r-limma" ,r-limma)
+ ("r-lumi" ,r-lumi)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-methylumi" ,r-methylumi)
+ ("r-roc" ,r-roc)))
+ (home-page "https://bioconductor.org/packages/wateRmelon/")
+ (synopsis "Illumina 450 methylation array normalization and metrics")
+ (description
+ "The standard index of DNA methylation (beta) is computed from methylated
+and unmethylated signal intensities. Betas calculated from raw signal
+intensities perform well, but using 11 methylomic datasets we demonstrate that
+quantile normalization methods produce marked improvement. The commonly used
+procedure of normalizing betas is inferior to the separate normalization of M
+and U, and it is also advantageous to normalize Type I and Type II assays
+separately. This package provides 15 flavours of betas and three performance
+metrics, with methods for objects produced by the @code{methylumi} and
+@code{minfi} packages.")
+ (license license:gpl3)))
+
+(define-public r-gdsfmt
+ (package
+ (name "r-gdsfmt")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gdsfmt" version))
+ (sha256
+ (base32
+ "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
+ (modules '((guix build utils)))
+ ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
+ ;; them and link with system libraries instead.
+ (snippet
+ '(begin
+ (for-each delete-file-recursively
+ '("src/LZ4"
+ "src/XZ"
+ "src/ZLIB"))
+ (substitute* "src/Makevars"
+ (("all: \\$\\(SHLIB\\)") "all:")
+ (("\\$\\(SHLIB\\): liblzma.a") "")
+ (("(ZLIB|LZ4)/.*") "")
+ (("CoreArray/dVLIntGDS.cpp.*")
+ "CoreArray/dVLIntGDS.cpp")
+ (("CoreArray/dVLIntGDS.o.*")
+ "CoreArray/dVLIntGDS.o")
+ (("PKG_LIBS = ./liblzma.a")
+ "PKG_LIBS = -llz4"))
+ (substitute* "src/CoreArray/dStream.h"
+ (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
+ (string-append "include <" header ">")))
+ #t))))
+ (properties `((upstream-name . "gdsfmt")))
+ (build-system r-build-system)
+ (inputs
+ `(("lz4" ,lz4)
+ ("xz" ,xz)
+ ("zlib" ,zlib)))
+ (home-page "http://corearray.sourceforge.net/")
+ (synopsis
+ "R Interface to CoreArray Genomic Data Structure (GDS) Files")
+ (description
+ "This package provides a high-level R interface to CoreArray @dfn{Genomic
+Data Structure} (GDS) data files, which are portable across platforms with
+hierarchical structure to store multiple scalable array-oriented data sets
+with metadata information. It is suited for large-scale datasets, especially
+for data which are much larger than the available random-access memory. The
+@code{gdsfmt} package offers efficient operations specifically designed for
+integers of less than 8 bits, since a diploid genotype, like
+@dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
+byte. Data compression and decompression are available with relatively
+efficient random access. It is also allowed to read a GDS file in parallel
+with multiple R processes supported by the package @code{parallel}.")
+ (license license:lgpl3)))
+
+(define-public r-bigmelon
+ (package
+ (name "r-bigmelon")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bigmelon" version))
+ (sha256
+ (base32
+ "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
+ (properties `((upstream-name . "bigmelon")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-gdsfmt" ,r-gdsfmt)
+ ("r-geoquery" ,r-geoquery)
+ ("r-methylumi" ,r-methylumi)
+ ("r-minfi" ,r-minfi)
+ ("r-watermelon" ,r-watermelon)))
+ (home-page "https://bioconductor.org/packages/bigmelon/")
+ (synopsis "Illumina methylation array analysis for large experiments")
+ (description
+ "This package provides methods for working with Illumina arrays using the
+@code{gdsfmt} package.")
+ (license license:gpl3)))
+
+(define-public r-seqbias
+ (package
+ (name "r-seqbias")
+ (version "1.32.0")
+ (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 "1.14.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "variancePartition" version))
+ (sha256
+ (base32
+ "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd"))))
+ (properties
+ `((upstream-name . "variancePartition")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocparallel" ,r-biocparallel)
+ ("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+)))
+
+(define-public r-htqpcr
+ (package
+ (name "r-htqpcr")
+ (version "1.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "HTqPCR" version))
+ (sha256
+ (base32
+ "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7"))))
+ (properties `((upstream-name . "HTqPCR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-biobase" ,r-biobase)
+ ("r-gplots" ,r-gplots)
+ ("r-limma" ,r-limma)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "http://www.ebi.ac.uk/bertone/software")
+ (synopsis "Automated analysis of high-throughput qPCR data")
+ (description
+ "Analysis of Ct values from high throughput quantitative real-time
+PCR (qPCR) assays across multiple conditions or replicates. The input data
+can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
+OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
+Laboratories; conventional 96- or 384-well plates; or microfluidic devices
+such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
+loading, quality assessment, normalization, visualization and parametric or
+non-parametric testing for statistical significance in Ct values between
+features (e.g. genes, microRNAs).")
+ (license license:artistic2.0)))
+
+(define-public r-unifiedwmwqpcr
+ (package
+ (name "r-unifiedwmwqpcr")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "unifiedWMWqPCR" version))
+ (sha256
+ (base32
+ "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a"))))
+ (properties
+ `((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+)))
HCoop / jackhill / guix / guix.git / blobdiff