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-rw-r--r--gnu/packages/bioconductor.scm278
1 files changed, 277 insertions, 1 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 68d8e5b574..b4be8aee15 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
;;;
@@ -493,6 +493,30 @@ annotations for the genome of the model mouse Mus musculus.")
by UCSC (hg19, February 2009) and stored in Biostrings objects.")
(license license:artistic2.0)))
+(define-public r-bsgenome-hsapiens-ucsc-hg38
+ (package
+ (name "r-bsgenome-hsapiens-ucsc-hg38")
+ (version "1.4.1")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
+ version 'annotation))
+ (sha256
+ (base32
+ "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
+ (properties
+ `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
+ (synopsis "Full genome sequences for Homo sapiens")
+ (description
+ "This package provides full genome sequences for Homo sapiens (Human)
+as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
+ (license license:artistic2.0)))
+
(define-public r-ensdb-hsapiens-v75
(package
(name "r-ensdb-hsapiens-v75")
@@ -718,6 +742,30 @@ annotations.")
"This is a manifest package for Illumina's EPIC methylation arrays.")
(license license:artistic2.0)))
+(define-public r-ideoviz
+ (package
+ (name "r-ideoviz")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "IdeoViz" version))
+ (sha256
+ (base32
+ "0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-iranges" ,r-iranges)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-genomeinfodb" ,r-genomeinfodb)))
+ (home-page "https://bioconductor.org/packages/IdeoViz/")
+ (synopsis "Plots data along a chromosomal ideogram")
+ (description "This package provides functions to plot data associated with
+arbitrary genomic intervals along chromosomal ideogram.")
+ (license license:gpl2)))
+
;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
;; from Bioconductor.
(define-public r-deconstructsigs
@@ -811,6 +859,32 @@ performing parallel computations on multicore machines.")
Disease Ontology.")
(license license:artistic2.0)))
+(define-public r-pasilla
+ (package
+ (name "r-pasilla")
+ (version "1.14.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://bioconductor.org/packages/release/data/experiment"
+ "/src/contrib/pasilla_" version ".tar.gz"))
+ (sha256
+ (base32
+ "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocstyle" ,r-biocstyle)
+ ("r-dexseq" ,r-dexseq)
+ ("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)))
+ (home-page "https://www.bioconductor.org/packages/pasilla/")
+ (synopsis "Data package with per-exon and per-gene read counts")
+ (description "This package provides per-exon and per-gene read counts
+computed for selected genes from RNA-seq data that were presented in the
+article 'Conservation of an RNA regulatory map between Drosophila and mammals'
+by Brooks et al., Genome Research 2011.")
+ (license license:lgpl2.1+)))
+
(define-public r-pfam-db
(package
(name "r-pfam-db")
@@ -995,6 +1069,63 @@ examples' of Affymetrix data, unlike the artificial examples included in the
package @code{affy}.")
(license license:gpl2+)))
+(define-public r-coverageview
+ (package
+ (name "r-coverageview")
+ (version "1.24.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CoverageView" version))
+ (sha256
+ (base32
+ "0s47svs7xnr9jkylq0dxidqrigihdddiprcl0951vjr4w7kmb5nf"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-s4vectors" ,r-s4vectors)
+ ("r-iranges" ,r-iranges)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-rsamtools" ,r-rsamtools)))
+ (home-page "https://bioconductor.org/packages/CoverageView/")
+ (synopsis "Coverage visualization package for R")
+ (description "This package provides a framework for the visualization of
+genome coverage profiles. It can be used for ChIP-seq experiments, but it can
+be also used for genome-wide nucleosome positioning experiments or other
+experiment types where it is important to have a framework in order to inspect
+how the coverage distributed across the genome.")
+ (license license:artistic2.0)))
+
+(define-public r-cummerbund
+ (package
+ (name "r-cummerbund")
+ (version "2.28.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "cummeRbund" version))
+ (sha256
+ (base32
+ "1fjc3bcclm4gsvw4nq6cv3a1kbrldvrxbkyfb9306708si1n4dwk"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-fastcluster", r-fastcluster)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gviz" ,r-gviz)
+ ("r-plyr" ,r-plyr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/cummeRbund/")
+ (synopsis "Analyze Cufflinks high-throughput sequencing data")
+ (description "This package allows for persistent storage, access,
+exploration, and manipulation of Cufflinks high-throughput sequencing
+data. In addition, provides numerous plotting functions for commonly
+used visualizations.")
+ (license license:artistic2.0)))
+
(define-public r-curatedtcgadata
(package
(name "r-curatedtcgadata")
@@ -2533,6 +2664,41 @@ and regression inferences from RNA-sequencing data.")
gene and isoform level using RNA-seq data")
(license license:artistic2.0)))
+(define-public r-karyoploter
+ (package
+ (name "r-karyoploter")
+ (version "1.12.4")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "karyoploteR" version))
+ (sha256
+ (base32
+ "03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-regioner" ,r-regioner)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-memoise" ,r-memoise)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-biovizbase" ,r-biovizbase)
+ ("r-digest" ,r-digest)
+ ("r-bezier" ,r-bezier)
+ ("r-bamsignals" ,r-bamsignals)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/karyoploteR/")
+ (synopsis "Plot customizable linear genomes displaying arbitrary data")
+ (description "This package creates karyotype plots of arbitrary genomes and
+offers a complete set of functions to plot arbitrary data on them. It mimicks
+many R base graphics functions coupling them with a coordinate change function
+automatically mapping the chromosome and data coordinates into the plot
+coordinates.")
+ (license license:artistic2.0)))
+
(define-public r-lpsymphony
(package
(name "r-lpsymphony")
@@ -3972,6 +4138,78 @@ database (e.g. JASPAR). It can also be used to visualize motifs, motif
distributions, modules and filter motifs.")
(license license:gpl2)))
+(define-public r-motifdb
+ (package
+ (name "r-motifdb")
+ (version "1.28.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MotifDb" version))
+ (sha256
+ (base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc"))))
+ (properties `((upstream-name . "MotifDb")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-iranges" ,r-iranges)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-splitstackshape" ,r-splitstackshape)))
+ (home-page "https://www.bioconductor.org/packages/MotifDb/")
+ (synopsis "Annotated collection of protein-DNA binding sequence motifs")
+ (description "This package provides more than 2000 annotated position
+frequency matrices from nine public sources, for multiple organisms.")
+ (license license:artistic2.0)))
+
+(define-public r-motifbreakr
+ (package
+ (name "r-motifbreakr")
+ (version "2.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "motifbreakR" version))
+ (sha256
+ (base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n"))))
+ (properties `((upstream-name . "motifbreakR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-grimport" ,r-grimport)
+ ("r-stringr" ,r-stringr)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-iranges" ,r-iranges)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-variantannotation" ,r-variantannotation)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-motifstack" ,r-motifstack)
+ ("r-gviz" ,r-gviz)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-tfmpvalue" ,r-tfmpvalue)
+ ("r-motifdb" ,r-motifdb)))
+ (home-page "https://www.bioconductor.org/packages/motifbreakR/")
+ (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
+ (description "This package allows biologists to judge in the first place
+whether the sequence surrounding the polymorphism is a good match, and in
+the second place how much information is gained or lost in one allele of
+the polymorphism relative to another. This package gives a choice of
+algorithms for interrogation of genomes with motifs from public sources:
+@enumerate
+@item a weighted-sum probability matrix;
+@item log-probabilities;
+@item weighted by relative entropy.
+@end enumerate
+
+This package can predict effects for novel or previously described variants in
+public databases, making it suitable for tasks beyond the scope of its original
+design. Lastly, it can be used to interrogate any genome curated within
+Bioconductor.")
+ (license license:gpl2+)))
+
(define-public r-motifstack
(package
(name "r-motifstack")
@@ -6368,6 +6606,44 @@ and parameters of which are trained on a set of aligned reads and a reference
genome sequence.")
(license license:lgpl3)))
+(define-public r-snplocs-hsapiens-dbsnp144-grch37
+ (package
+ (name "r-snplocs-hsapiens-dbsnp144-grch37")
+ (version "0.99.20")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
+ version 'annotation))
+ (sha256
+ (base32
+ "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-iranges" ,r-iranges)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-biostrings" ,r-biostrings)))
+ (home-page
+ "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
+ (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
+ (description "This package provides SNP locations and alleles for Homo
+sapiens extracted from NCBI dbSNP Build 144. The source data files used for
+this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
+to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
+patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
+X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
+the mitochondrion chromosome. Therefore, the SNPs in this package can be
+injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
+correct position but this injection will exclude chrM (i.e. nothing will be
+injected in that sequence).")
+ (license license:artistic2.0)))
+
(define-public r-reqon
(package
(name "r-reqon")