aboutsummaryrefslogtreecommitdiff
path: root/gnu/packages/bioconductor.scm
diff options
context:
space:
mode:
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r--gnu/packages/bioconductor.scm161
1 files changed, 123 insertions, 38 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a6e0c5a1e6..63687036fc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -224,6 +224,30 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
(license license:artistic2.0)))
+(define-public r-bsgenome-hsapiens-ncbi-grch38
+ (package
+ (name "r-bsgenome-hsapiens-ncbi-grch38")
+ (version "1.3.1000")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
+ version 'annotation))
+ (sha256
+ (base32
+ "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
+ (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "https://bioconductor.org/packages/release/data/annotation/html/\
+BSgenome.Hsapiens.NCBI.GRCh38.html")
+ (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
+ (description
+ "This package provides full genome sequences for Homo sapiens (Human) as
+provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
+ (license license:artistic2.0)))
+
(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
(package
(name "r-bsgenome-hsapiens-ucsc-hg19-masked")
@@ -594,14 +618,14 @@ database is exposed as a @code{TxDb} object.")
(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
(package
(name "r-txdb-mmusculus-ucsc-mm10-knowngene")
- (version "3.4.7")
+ (version "3.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
version 'annotation))
(sha256
(base32
- "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
+ "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
(properties
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(build-system r-build-system)
@@ -722,6 +746,49 @@ the weighted combination of published signatures that, when summed, most
closely reconstructs the mutational profile.")
(license license:gpl2+)))
+;; This is a CRAN package, but it depends on Bioconductor packages.
+(define-public r-nmf
+ (package
+ (name "r-nmf")
+ (version "0.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "NMF" version))
+ (sha256
+ (base32
+ "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq"))))
+ (properties `((upstream-name . "NMF")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cluster" ,r-cluster)
+ ("r-biobase" ,r-biobase)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-bigmemory" ,r-bigmemory) ; suggested
+ ("r-synchronicity" ,r-synchronicity) ; suggested
+ ("r-colorspace" ,r-colorspace)
+ ("r-digest" ,r-digest)
+ ("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridbase" ,r-gridbase)
+ ("r-pkgmaker" ,r-pkgmaker)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-registry" ,r-registry)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rngtools" ,r-rngtools)
+ ("r-stringr" ,r-stringr)))
+ (home-page "http://renozao.github.io/NMF")
+ (synopsis "Algorithms and framework for nonnegative matrix factorization")
+ (description
+ "This package provides a framework to perform Non-negative Matrix
+Factorization (NMF). The package implements a set of already published
+algorithms and seeding methods, and provides a framework to test, develop and
+plug new or custom algorithms. Most of the built-in algorithms have been
+optimized in C++, and the main interface function provides an easy way of
+performing parallel computations on multicore machines.")
+ (license license:gpl2+)))
+
(define-public r-do-db
(package
(name "r-do-db")
@@ -1526,6 +1593,30 @@ expressed genes in DNA microarray experiments.")
"This package implements some simple graph handling capabilities for R.")
(license license:artistic2.0)))
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-ggm
+ (package
+ (name "r-ggm")
+ (version "2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ggm" version))
+ (sha256
+ (base32
+ "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
+ (properties `((upstream-name . "ggm")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-graph" ,r-graph)
+ ("r-igraph" ,r-igraph)))
+ (home-page "https://cran.r-project.org/package=ggm")
+ (synopsis "Functions for graphical Markov models")
+ (description
+ "This package provides functions and datasets for maximum likelihood
+fitting of some classes of graphical Markov models.")
+ (license license:gpl2+)))
+
(define-public r-codedepends
(package
(name "r-codedepends")
@@ -1557,14 +1648,14 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.20.0")
+ (version "3.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa"))))
+ "0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
@@ -1867,14 +1958,14 @@ experiments.")
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.20.0")
+ (version "1.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc"))))
+ "140bp7c8p079xh5wwxmrq3a73pm6mdc9czq5w2gzjml7dgrca38a"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
@@ -2028,14 +2119,14 @@ genes or proteins in these datasets.")
(define-public r-inspect
(package
(name "r-inspect")
- (version "1.16.2")
+ (version "1.16.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "INSPEcT" version))
(sha256
(base32
- "1g8la7k4pnyr2hvk4yjd1bwvjy6nqbbb0fwxrrh2ifgqf4h21x2p"))))
+ "0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp"))))
(properties `((upstream-name . "INSPEcT")))
(build-system r-build-system)
(propagated-inputs
@@ -2125,14 +2216,14 @@ samples.")
(define-public r-biocneighbors
(package
(name "r-biocneighbors")
- (version "1.4.1")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocNeighbors" version))
(sha256
(base32
- "05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf"))))
+ "1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6"))))
(properties `((upstream-name . "BiocNeighbors")))
(build-system r-build-system)
(propagated-inputs
@@ -2156,14 +2247,14 @@ achieved for all methods using the BiocParallel framework.")
(define-public r-biocsingular
(package
(name "r-biocsingular")
- (version "1.2.1")
+ (version "1.2.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocSingular" version))
(sha256
(base32
- "0fjfmmpda7pszsck2hm7bp4509pl3xaz02q2q03d5vla62h1h81k"))))
+ "1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407"))))
(properties `((upstream-name . "BiocSingular")))
(build-system r-build-system)
(propagated-inputs
@@ -3130,27 +3221,20 @@ surface of a flowcell.")
(define-public r-gkmsvm
(package
(name "r-gkmsvm")
- (version "0.79.0")
+ (version "0.80.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "gkmSVM" version))
(sha256
(base32
- "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
+ "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p"))))
(properties `((upstream-name . "gkmSVM")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-kernlab" ,r-kernlab)
+ `(("r-kernlab" ,r-kernlab)
("r-rcpp" ,r-rcpp)
("r-rocr" ,r-rocr)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
("r-seqinr" ,r-seqinr)))
(home-page "https://cran.r-project.org/web/packages/gkmSVM")
(synopsis "Gapped-kmer support vector machine")
@@ -3284,14 +3368,14 @@ gmapR.")
(define-public r-heatplus
(package
(name "r-heatplus")
- (version "2.32.0")
+ (version "2.32.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Heatplus" version))
(sha256
(base32
- "0hx5gqgh4xrkx37ccprq7azj9jziff137bdk0gvrixcx52ws6h89"))))
+ "1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1"))))
(properties `((upstream-name . "Heatplus")))
(build-system r-build-system)
(propagated-inputs
@@ -3521,14 +3605,14 @@ profiles (GO and KEGG) of gene and gene clusters.")
(define-public r-mlinterfaces
(package
(name "r-mlinterfaces")
- (version "1.66.2")
+ (version "1.66.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MLInterfaces" version))
(sha256
(base32
- "1wc280iw9vllg6f58vsdj895yaqs8w42kl7jk8sgii009gwlaj8d"))))
+ "19hlicdndy2p45y7w91gnwi3wgq5s465a646z3qqk8gmn5sn614q"))))
(properties `((upstream-name . "MLInterfaces")))
(build-system r-build-system)
(propagated-inputs
@@ -3942,14 +4026,14 @@ position-specific scores within R and Bioconductor.")
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
- (version "1.10.1")
+ (version "1.10.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
- "12ix0bvwk50d48z85f3453k7szm1j27gk4qgw56az4fxra472rlh"))))
+ "0dzrizacy3br8fiy1vnsl5zf242lg1hqv9dyv5ayqh2n480is57f"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
@@ -5305,14 +5389,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "2.0.0")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "0l8q9y2a4m1di0w5nlxhq9jgliinhgr2fwjpm5ixnqx5j3iprlwd"))))
+ "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -5817,14 +5901,14 @@ self-organizing map clustering and minimal spanning trees.")
(define-public r-mixomics
(package
(name "r-mixomics")
- (version "6.10.6")
+ (version "6.10.8")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
- "18jwrdyc4pnx917y1kskxz3fqvlrkyy4ny0xqrfcidz0j7p0b7wr"))))
+ "0307vhx9ck24rxqbvq15815ssxcc226sl2la060n204b51wi9jaa"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
@@ -5859,14 +5943,14 @@ delete entire rows with missing data.")
(define-public r-depecher
(package
(name "r-depecher")
- (version "1.2.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DepecheR" version))
(sha256
(base32
- "1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5"))))
+ "08ja6ayvbax9m3x9w3xzi72z97miiha2nbsild1gp77n6sgn5i35"))))
(properties `((upstream-name . "DepecheR")))
(build-system r-build-system)
(propagated-inputs
@@ -5937,14 +6021,14 @@ genes in the gene-set that are ranked above the leading edge).")
(define-public r-cicero
(package
(name "r-cicero")
- (version "1.4.0")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cicero" version))
(sha256
(base32
- "0mmm7vvzq50b5fayid0bw82b5lar3xm9fwl2ya30q0p4db2y6wnz"))))
+ "154djqd32w87814ycfmfz27ikp17bnampvmvw5hzi5p2x9l3h82r"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -5966,6 +6050,7 @@ genes in the gene-set that are ranked above the leading edge).")
("r-s4vectors" ,r-s4vectors)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
("r-vgam" ,r-vgam)))
(home-page "https://bioconductor.org/packages/cicero/")
(synopsis "Predict cis-co-accessibility from single-cell data")
@@ -7205,14 +7290,14 @@ access.")
(define-public r-multiassayexperiment
(package
(name "r-multiassayexperiment")
- (version "1.12.2")
+ (version "1.12.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiAssayExperiment" version))
(sha256
(base32
- "0722f3jl1xq8k8w7vrv986jd16bgysqp3n07pgmdn0hh1zh2mcqc"))))
+ "1vf6l88j3n6109j6sd08wfqxqpj2k20dvr8ll9zl1szsn18b4gny"))))
(properties
`((upstream-name . "MultiAssayExperiment")))
(build-system r-build-system)