#:use-module (gnu packages compression)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
+ #:use-module (gnu packages haskell)
+ #: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))
\f
;;; Experiment data
+(define-public r-abadata
+ (package
+ (name "r-abadata")
+ (version "1.12.0")
+ (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/"
+ "ABAData_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
+ (properties
+ `((upstream-name . "ABAData")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://www.bioconductor.org/packages/ABAData/")
+ (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
+ (description
+ "This package provides the data for the gene expression enrichment
+analysis conducted in the package ABAEnrichment. The package includes three
+datasets which are derived from the Allen Brain Atlas:
+
+@enumerate
+@item Gene expression data from Human Brain (adults) averaged across donors,
+@item Gene expression data from the Developing Human Brain pooled into five
+ age categories and averaged across donors, and
+@item a developmental effect score based on the Developing Human Brain
+ expression data.
+@end enumerate
+
+All datasets are restricted to protein coding genes.")
+ (license license:gpl2+)))
+
+(define-public r-arrmdata
+ (package
+ (name "r-arrmdata")
+ (version "1.18.0")
+ (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/"
+ "ARRmData_" version ".tar.gz"))
+ (sha256
+ (base32
+ "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
+ (properties
+ `((upstream-name . "ARRmData")))
+ (build-system r-build-system)
+ (home-page "https://www.bioconductor.org/packages/ARRmData/")
+ (synopsis "Example dataset for normalization of Illumina 450k methylation data")
+ (description
+ "This package provides raw beta values from 36 samples across 3 groups
+from Illumina 450k methylation arrays.")
+ (license license:artistic2.0)))
+
(define-public r-hsmmsinglecell
(package
(name "r-hsmmsinglecell")
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
- (version "0.28.0")
+ (version "0.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocGenerics" version))
(sha256
(base32
- "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
+ "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
(properties
`((upstream-name . "BiocGenerics")))
(build-system r-build-system)
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.60.1")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"))))
+ "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public r-hpar
(package
(name "r-hpar")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hpar" version))
(sha256
(base32
- "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
+ "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/hpar/")
(synopsis "Human Protein Atlas in R")
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
+ "014h2q346ynfdbpavh4p69cyv4j65hk934liq5892zznjzl73z7p"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-geneplotter
(package
(name "r-geneplotter")
- (version "1.60.0")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geneplotter" version))
(sha256
(base32
- "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
+ "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
(define-public r-qvalue
(package
(name "r-qvalue")
- (version "2.14.1")
+ (version "2.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "qvalue" version))
(sha256
(base32
- "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
+ "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
(define-public r-diffbind
(package
(name "r-diffbind")
- (version "2.10.0")
+ (version "2.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
- "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
+ "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(inputs
("r-locfit" ,r-locfit)
("r-rcolorbrewer" , r-rcolorbrewer)
("r-rcpp" ,r-rcpp)
+ ("r-rhtslib" ,r-rhtslib)
("r-rsamtools" ,r-rsamtools)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-systempiper" ,r-systempiper)
- ("r-zlibbioc" ,r-zlibbioc)))
+ ("r-systempiper" ,r-systempiper)))
(home-page "http://bioconductor.org/packages/DiffBind")
(synopsis "Differential binding analysis of ChIP-Seq peak data")
(description
(define-public r-ripseeker
(package
(name "r-ripseeker")
- (version "1.22.0")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RIPSeeker" version))
(sha256
(base32
- "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
+ "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
(properties `((upstream-name . "RIPSeeker")))
(build-system r-build-system)
(propagated-inputs
(define-public r-multtest
(package
(name "r-multtest")
- (version "2.38.0")
+ (version "2.40.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "multtest" version))
(sha256
(base32
- "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
+ "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-survival" ,r-survival)
(define-public r-graph
(package
(name "r-graph")
- (version "1.60.0")
+ (version "1.62.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "graph" version))
(sha256
(base32
- "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
+ "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
(define-public r-marray
(package
(name "r-marray")
- (version "1.60.0")
+ (version "1.62.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
- (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
+ (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-limma" ,r-limma)))
(define-public r-cghbase
(package
(name "r-cghbase")
- (version "1.42.0")
+ (version "1.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
- (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
+ (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
(define-public r-cghcall
(package
(name "r-cghcall")
- (version "2.44.0")
+ (version "2.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
- (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
+ (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
- (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
+ (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-bayseq
(package
(name "r-bayseq")
- (version "2.16.0")
+ (version "2.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "baySeq" version))
(sha256
(base32
- "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
+ "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
(properties `((upstream-name . "baySeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-chipcomp
(package
(name "r-chipcomp")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPComp" version))
(sha256
(base32
- "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
+ "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
(properties `((upstream-name . "ChIPComp")))
(build-system r-build-system)
(propagated-inputs
(define-public r-riboprofiling
(package
(name "r-riboprofiling")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RiboProfiling" version))
(sha256
(base32
- "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
+ "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
(properties `((upstream-name . "RiboProfiling")))
(build-system r-build-system)
(propagated-inputs
(define-public r-riboseqr
(package
(name "r-riboseqr")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "riboSeqR" version))
(sha256
(base32
- "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
+ "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
(properties `((upstream-name . "riboSeqR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-interactionset
(package
(name "r-interactionset")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "InteractionSet" version))
(sha256
(base32
- "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
+ "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
(properties
`((upstream-name . "InteractionSet")))
(build-system r-build-system)
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
+ "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
(define-public r-ctc
(package
(name "r-ctc")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ctc" version))
(sha256
(base32
- "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
+ "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
(build-system r-build-system)
(propagated-inputs `(("r-amap" ,r-amap)))
(home-page "https://bioconductor.org/packages/ctc/")
(define-public r-goseq
(package
(name "r-goseq")
- (version "1.34.1")
+ (version "1.36.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "goseq" version))
(sha256
(base32
- "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
+ "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public r-glimma
(package
(name "r-glimma")
- (version "1.10.1")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Glimma" version))
(sha256
(base32
- "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
+ "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
(properties `((upstream-name . "Glimma")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rots
(package
(name "r-rots")
- (version "1.10.1")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ROTS" version))
(sha256
(base32
- "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
+ "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
(properties `((upstream-name . "ROTS")))
(build-system r-build-system)
(propagated-inputs
(define-public r-plgem
(package
(name "r-plgem")
- (version "1.54.1")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "plgem" version))
(sha256
(base32
- "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
+ "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-inspect
(package
(name "r-inspect")
- (version "1.12.1")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "INSPEcT" version))
(sha256
(base32
- "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
+ "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
(properties `((upstream-name . "INSPEcT")))
(build-system r-build-system)
(propagated-inputs
(define-public r-dnabarcodes
(package
(name "r-dnabarcodes")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNABarcodes" version))
(sha256
(base32
- "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
+ "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
(properties `((upstream-name . "DNABarcodes")))
(build-system r-build-system)
(propagated-inputs
(define-public r-ruvseq
(package
(name "r-ruvseq")
- (version "1.16.1")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RUVSeq" version))
(sha256
(base32
- "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
+ "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
(properties `((upstream-name . "RUVSeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-biocneighbors
(package
(name "r-biocneighbors")
- (version "1.0.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocNeighbors" version))
(sha256
(base32
- "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
+ "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
(properties `((upstream-name . "BiocNeighbors")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
("r-rcpp" ,r-rcpp)
("r-rcppannoy" ,r-rcppannoy)
+ ("r-rcpphnsw" ,r-rcpphnsw)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://bioconductor.org/packages/BiocNeighbors")
(synopsis "Nearest Neighbor Detection for Bioconductor packages")
achieved for all methods using the BiocParallel framework.")
(license license:gpl3)))
+(define-public r-biocsingular
+ (package
+ (name "r-biocsingular")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocSingular" version))
+ (sha256
+ (base32
+ "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
+ (properties `((upstream-name . "BiocSingular")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beachmat" ,r-beachmat)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-irlba" ,r-irlba)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rsvd" ,r-rsvd)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/LTLA/BiocSingular")
+ (synopsis "Singular value decomposition for Bioconductor packages")
+ (description
+ "This package implements exact and approximate methods for singular value
+decomposition and principal components analysis, in a framework that allows
+them to be easily switched within Bioconductor packages or workflows. Where
+possible, parallelization is achieved using the BiocParallel framework.")
+ (license license:gpl3)))
+
(define-public r-destiny
(package
(name "r-destiny")
- (version "2.12.0")
+ (version "2.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "destiny" version))
(sha256
(base32
- "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
+ "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
- ("r-fnn" ,r-fnn)
+ ("r-ggplot2" ,r-ggplot2)
("r-ggthemes" ,r-ggthemes)
- ("r-hmisc" ,r-hmisc)
("r-igraph" ,r-igraph)
("r-matrix" ,r-matrix)
("r-proxy" ,r-proxy)
(define-public r-savr
(package
(name "r-savr")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "savR" version))
(sha256
(base32
- "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
+ "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
(properties `((upstream-name . "savR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-chipexoqual
(package
(name "r-chipexoqual")
- (version "1.6.0")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPexoQual" version))
(sha256
(base32
- "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
+ "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
(properties `((upstream-name . "ChIPexoQual")))
(build-system r-build-system)
(propagated-inputs
(define-public r-copynumber
(package
(name "r-copynumber")
- (version "1.22.0")
+ (version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "copynumber" version))
(sha256
(base32
- "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
+ "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
(define-public r-dnacopy
(package
(name "r-dnacopy")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNAcopy" version))
(sha256
(base32
- "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
+ "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
(properties `((upstream-name . "DNAcopy")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(define-public r-deds
(package
(name "r-deds")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEDS" version))
(sha256
(base32
- "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
+ "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
(properties `((upstream-name . "DEDS")))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/DEDS/")
(define-public r-ebseq
(package
(name "r-ebseq")
- (version "1.22.1")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EBSeq" version))
(sha256
(base32
- "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
+ "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
(properties `((upstream-name . "EBSeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-mlinterfaces
(package
(name "r-mlinterfaces")
- (version "1.62.0")
+ (version "1.62.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MLInterfaces" version))
(sha256
(base32
- "12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8"))))
+ "1h0x1p2h8x1h276wxx6kcnb4c4s5sglnmd58iigl81a224x8gxwp"))))
(properties `((upstream-name . "MLInterfaces")))
(build-system r-build-system)
(propagated-inputs
"This package provides basic features for the automated analysis of
Affymetrix arrays.")
(license license:gpl3)))
+
+(define-public r-a4
+ (package
+ (name "r-a4")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "a4" version))
+ (sha256
+ (base32
+ "1iqjy35rqx3m2y0dm2bk4cnzdm1qvbi608bfmrid88w6wmwz3qlk"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-a4base" ,r-a4base)
+ ("r-a4classif" ,r-a4classif)
+ ("r-a4core" ,r-a4core)
+ ("r-a4preproc" ,r-a4preproc)
+ ("r-a4reporting" ,r-a4reporting)))
+ (home-page "https://bioconductor.org/packages/a4/")
+ (synopsis "Automated Affymetrix array analysis umbrella package")
+ (description
+ "This package provides a software suite for the automated analysis of
+Affymetrix arrays.")
+ (license license:gpl3)))
+
+(define-public r-abseqr
+ (package
+ (name "r-abseqr")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "abseqR" version))
+ (sha256
+ (base32
+ "0w0ngxnilcrxlixsz7ls3zm99gyabxwn7w1r3r45n96d4aj075ry"))))
+ (properties `((upstream-name . "abseqR")))
+ (build-system r-build-system)
+ (inputs
+ `(("pandoc" ,ghc-pandoc)))
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-biocstyle" ,r-biocstyle)
+ ("r-circlize" ,r-circlize)
+ ("r-flexdashboard" ,r-flexdashboard)
+ ("r-ggcorrplot" ,r-ggcorrplot)
+ ("r-ggdendro" ,r-ggdendro)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-knitr" ,r-knitr)
+ ("r-plotly" ,r-plotly)
+ ("r-plyr" ,r-plyr)
+ ("r-png" ,r-png)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-stringr" ,r-stringr)
+ ("r-vegan" ,r-vegan)
+ ("r-venndiagram" ,r-venndiagram)))
+ (home-page "https://github.com/malhamdoosh/abseqR")
+ (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
+ (description
+ "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
+sequencing datasets generated from antibody libraries and abseqR is one of its
+packages. AbseqR empowers the users of abseqPy with plotting and reporting
+capabilities and allows them to generate interactive HTML reports for the
+convenience of viewing and sharing with other researchers. Additionally,
+abseqR extends abseqPy to compare multiple repertoire analyses and perform
+further downstream analysis on its output.")
+ (license license:gpl3)))
+
+(define-public r-bacon
+ (package
+ (name "r-bacon")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bacon" version))
+ (sha256
+ (base32
+ "1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-ellipse" ,r-ellipse)
+ ("r-ggplot2" ,r-ggplot2)))
+ (home-page "https://bioconductor.org/packages/bacon/")
+ (synopsis "Controlling bias and inflation in association studies")
+ (description
+ "Bacon can be used to remove inflation and bias often observed in
+epigenome- and transcriptome-wide association studies. To this end bacon
+constructs an empirical null distribution using a Gibbs Sampling algorithm by
+fitting a three-component normal mixture on z-scores.")
+ (license license:gpl2+)))
+
+(define-public r-rgadem
+ (package
+ (name "r-rgadem")
+ (version "2.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rGADEM" version))
+ (sha256
+ (base32
+ "1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2"))))
+ (properties `((upstream-name . "rGADEM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-iranges" ,r-iranges)
+ ("r-seqlogo" ,r-seqlogo)))
+ (home-page "https://bioconductor.org/packages/rGADEM/")
+ (synopsis "De novo sequence motif discovery")
+ (description
+ "rGADEM is an efficient de novo motif discovery tool for large-scale
+genomic sequence data.")
+ (license license:artistic2.0)))
+
+(define-public r-motiv
+ (package
+ (name "r-motiv")
+ (version "1.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MotIV" version))
+ (sha256
+ (base32
+ "1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8"))))
+ (properties `((upstream-name . "MotIV")))
+ (build-system r-build-system)
+ (inputs
+ `(("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-rgadem" ,r-rgadem)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/MotIV/")
+ (synopsis "Motif identification and validation")
+ (description
+ "This package is used for the identification and validation of sequence
+motifs. It makes use of STAMP for comparing a set of motifs to a given
+database (e.g. JASPAR). It can also be used to visualize motifs, motif
+distributions, modules and filter motifs.")
+ (license license:gpl2)))
+
+(define-public r-motifstack
+ (package
+ (name "r-motifstack")
+ (version "1.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "motifStack" version))
+ (sha256
+ (base32
+ "1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf"))))
+ (properties `((upstream-name . "motifStack")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ade4" ,r-ade4)
+ ("r-biostrings" ,r-biostrings)
+ ("r-grimport" ,r-grimport)
+ ("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-motiv" ,r-motiv)
+ ("r-scales" ,r-scales)
+ ("r-xml" ,r-xml)))
+ (home-page "https://bioconductor.org/packages/motifStack/")
+ (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
+ (description
+ "The motifStack package is designed for graphic representation of
+multiple motifs with different similarity scores. It works with both DNA/RNA
+sequence motifs and amino acid sequence motifs. In addition, it provides the
+flexibility for users to customize the graphic parameters such as the font
+type and symbol colors.")
+ (license license:gpl2+)))
+
+(define-public r-genomicscores
+ (package
+ (name "r-genomicscores")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicScores" version))
+ (sha256
+ (base32
+ "0lrhkcblvnki6kncwpavs01gbcz22yza6ma8zvfmbrrkfaxqzh8n"))))
+ (properties `((upstream-name . "GenomicScores")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationhub" ,r-annotationhub)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-xml" ,r-xml)))
+ (home-page "https://github.com/rcastelo/GenomicScores/")
+ (synopsis "Work with genome-wide position-specific scores")
+ (description
+ "This package provides infrastructure to store and access genome-wide
+position-specific scores within R and Bioconductor.")
+ (license license:artistic2.0)))
+
+(define-public r-atacseqqc
+ (package
+ (name "r-atacseqqc")
+ (version "1.6.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ATACseqQC" version))
+ (sha256
+ (base32
+ "1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn"))))
+ (properties `((upstream-name . "ATACseqQC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-chippeakanno" ,r-chippeakanno)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-genomicscores" ,r-genomicscores)
+ ("r-iranges" ,r-iranges)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-limma" ,r-limma)
+ ("r-motifstack" ,r-motifstack)
+ ("r-preseqr" ,r-preseqr)
+ ("r-randomforest" ,r-randomforest)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/ATACseqQC/")
+ (synopsis "ATAC-seq quality control")
+ (description
+ "ATAC-seq, an assay for Transposase-Accessible Chromatin using
+sequencing, is a rapid and sensitive method for chromatin accessibility
+analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
+and DNAse-seq. The ATACseqQC package was developed to help users to quickly
+assess whether their ATAC-seq experiment is successful. It includes
+diagnostic plots of fragment size distribution, proportion of mitochondria
+reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
+footprints.")
+ (license license:gpl2+)))
+
+(define-public r-gofuncr
+ (package
+ (name "r-gofuncr")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GOfuncR" version))
+ (sha256
+ (base32
+ "021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk"))))
+ (properties `((upstream-name . "GOfuncR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-mapplots" ,r-mapplots)
+ ("r-rcpp" ,r-rcpp)
+ ("r-vioplot" ,r-vioplot)))
+ (home-page "https://bioconductor.org/packages/GOfuncR/")
+ (synopsis "Gene ontology enrichment using FUNC")
+ (description
+ "GOfuncR performs a gene ontology enrichment analysis based on the
+ontology enrichment software FUNC. GO-annotations are obtained from
+OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
+included in the package and updated regularly. GOfuncR provides the standard
+candidate vs background enrichment analysis using the hypergeometric test, as
+well as three additional tests:
+
+@enumerate
+@item the Wilcoxon rank-sum test that is used when genes are ranked,
+@item a binomial test that is used when genes are associated with two counts,
+ and
+@item a Chi-square or Fisher's exact test that is used in cases when genes are
+associated with four counts.
+@end enumerate
+
+To correct for multiple testing and interdependency of the tests, family-wise
+error rates are computed based on random permutations of the gene-associated
+variables. GOfuncR also provides tools for exploring the ontology graph and
+the annotations, and options to take gene-length or spatial clustering of
+genes into account. It is also possible to provide custom gene coordinates,
+annotations and ontologies.")
+ (license license:gpl2+)))
+
+(define-public r-abaenrichment
+ (package
+ (name "r-abaenrichment")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ABAEnrichment" version))
+ (sha256
+ (base32
+ "0bvanqmg1smyckh16m2qn7d68zq4j7n74sgsnbgms5jngbp9158v"))))
+ (properties `((upstream-name . "ABAEnrichment")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-abadata" ,r-abadata)
+ ("r-data-table" ,r-data-table)
+ ("r-gofuncr" ,r-gofuncr)
+ ("r-gplots" ,r-gplots)
+ ("r-gtools" ,r-gtools)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://bioconductor.org/packages/ABAEnrichment/")
+ (synopsis "Gene expression enrichment in human brain regions")
+ (description
+ "The package ABAEnrichment is designed to test for enrichment of user
+defined candidate genes in the set of expressed genes in different human brain
+regions. The core function @code{aba_enrich} integrates the expression of the
+candidate gene set (averaged across donors) and the structural information of
+the brain using an ontology, both provided by the Allen Brain Atlas project.")
+ (license license:gpl2+)))
+
+(define-public r-annotationfuncs
+ (package
+ (name "r-annotationfuncs")
+ (version "1.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationFuncs" version))
+ (sha256
+ (base32
+ "1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss"))))
+ (properties
+ `((upstream-name . "AnnotationFuncs")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-dbi" ,r-dbi)))
+ (home-page "https://www.iysik.com/r/annotationfuncs")
+ (synopsis "Annotation translation functions")
+ (description
+ "This package provides functions for handling translating between
+different identifieres using the Biocore Data Team data-packages (e.g.
+@code{org.Bt.eg.db}).")
+ (license license:gpl2)))
+
+(define-public r-annotationtools
+ (package
+ (name "r-annotationtools")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "annotationTools" version))
+ (sha256
+ (base32
+ "0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z"))))
+ (properties
+ `((upstream-name . "annotationTools")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-biobase" ,r-biobase)))
+ (home-page "https://bioconductor.org/packages/annotationTools/")
+ (synopsis "Annotate microarrays and perform gene expression analyses")
+ (description
+ "This package provides functions to annotate microarrays, find orthologs,
+and integrate heterogeneous gene expression profiles using annotation and
+other molecular biology information available as flat file database (plain
+text files).")
+ ;; Any version of the GPL.
+ (license (list license:gpl2+))))
+
+(define-public r-allelicimbalance
+ (package
+ (name "r-allelicimbalance")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AllelicImbalance" version))
+ (sha256
+ (base32
+ "03524lj6aw9cskbpxzjmi9g708x6p94mf26yz4j941g1d0mc3z91"))))
+ (properties
+ `((upstream-name . "AllelicImbalance")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gviz" ,r-gviz)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-latticeextra" ,r-latticeextra)
+ ("r-nlme" ,r-nlme)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqinr" ,r-seqinr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://github.com/pappewaio/AllelicImbalance")
+ (synopsis "Investigate allele-specific expression")
+ (description
+ "This package provides a framework for allele-specific expression
+investigation using RNA-seq data.")
+ (license license:gpl3)))
+
+(define-public r-aucell
+ (package
+ (name "r-aucell")
+ (version "1.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AUCell" version))
+ (sha256
+ (base32
+ "1kdrs0521cyb8wlc4i3idfprrcy2f9w6kl56hfa94n0brmx62ya9"))))
+ (properties `((upstream-name . "AUCell")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-gseabase" ,r-gseabase)
+ ("r-mixtools" ,r-mixtools)
+ ("r-r-utils" ,r-r-utils)
+ ("r-shiny" ,r-shiny)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/AUCell/")
+ (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
+ (description
+ "AUCell allows to identify cells with active gene sets (e.g. signatures,
+gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
+Under the Curve} (AUC) to calculate whether a critical subset of the input
+gene set is enriched within the expressed genes for each cell. The
+distribution of AUC scores across all the cells allows exploring the relative
+expression of the signature. Since the scoring method is ranking-based,
+AUCell is independent of the gene expression units and the normalization
+procedure. In addition, since the cells are evaluated individually, it can
+easily be applied to bigger datasets, subsetting the expression matrix if
+needed.")
+ (license license:gpl3)))
+
+(define-public r-ebimage
+ (package
+ (name "r-ebimage")
+ (version "4.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "EBImage" version))
+ (sha256
+ (base32
+ "18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx"))))
+ (properties `((upstream-name . "EBImage")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-abind" ,r-abind)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-fftwtools" ,r-fftwtools)
+ ("r-htmltools" ,r-htmltools)
+ ("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-jpeg" ,r-jpeg)
+ ("r-locfit" ,r-locfit)
+ ("r-png" ,r-png)
+ ("r-rcurl" ,r-rcurl)
+ ("r-tiff" ,r-tiff)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
+ (home-page "https://github.com/aoles/EBImage")
+ (synopsis "Image processing and analysis toolbox for R")
+ (description
+ "EBImage provides general purpose functionality for image processing and
+analysis. In the context of (high-throughput) microscopy-based cellular
+assays, EBImage offers tools to segment cells and extract quantitative
+cellular descriptors. This allows the automation of such tasks using the R
+programming language and facilitates the use of other tools in the R
+environment for signal processing, statistical modeling, machine learning and
+visualization with image data.")
+ ;; Any version of the LGPL.
+ (license license:lgpl2.1+)))
+
+(define-public r-yamss
+ (package
+ (name "r-yamss")
+ (version "1.8.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "yamss" version))
+ (sha256
+ (base32
+ "13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-data-table" ,r-data-table)
+ ("r-ebimage" ,r-ebimage)
+ ("r-iranges" ,r-iranges)
+ ("r-limma" ,r-limma)
+ ("r-matrix" ,r-matrix)
+ ("r-mzr" ,r-mzr)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment"
+ ,r-summarizedexperiment)))
+ (home-page "https://github.com/hansenlab/yamss")
+ (synopsis "Tools for high-throughput metabolomics")
+ (description
+ "This package provides tools to analyze and visualize high-throughput
+metabolomics data acquired using chromatography-mass spectrometry. These tools
+preprocess data in a way that enables reliable and powerful differential
+analysis.")
+ (license license:artistic2.0)))
+
+(define-public r-gtrellis
+ (package
+ (name "r-gtrellis")
+ (version "1.14.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gtrellis" version))
+ (sha256
+ (base32
+ "17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-circlize" ,r-circlize)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-getoptlong" ,r-getoptlong)
+ ("r-iranges" ,r-iranges)))
+ (home-page "https://github.com/jokergoo/gtrellis")
+ (synopsis "Genome level Trellis layout")
+ (description
+ "Genome level Trellis graph visualizes genomic data conditioned by
+genomic categories (e.g. chromosomes). For each genomic category, multiple
+dimensional data which are represented as tracks describe different features
+from different aspects. This package provides high flexibility to arrange
+genomic categories and to add self-defined graphics in the plot.")
+ (license license:expat)))
+
+(define-public r-somaticsignatures
+ (package
+ (name "r-somaticsignatures")
+ (version "2.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "SomaticSignatures" version))
+ (sha256
+ (base32
+ "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02"))))
+ (properties
+ `((upstream-name . "SomaticSignatures")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbio" ,r-ggbio)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-nmf" ,r-nmf)
+ ("r-pcamethods" ,r-pcamethods)
+ ("r-proxy" ,r-proxy)
+ ("r-reshape2" ,r-reshape2)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://github.com/juliangehring/SomaticSignatures")
+ (synopsis "Somatic signatures")
+ (description
+ "This package identifies mutational signatures of @dfn{single nucleotide
+variants} (SNVs). It provides a infrastructure related to the methodology
+described in Nik-Zainal (2012, Cell), with flexibility in the matrix
+decomposition algorithms.")
+ (license license:expat)))
+
+(define-public r-yapsa
+ (package
+ (name "r-yapsa")
+ (version "1.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "YAPSA" version))
+ (sha256
+ (base32
+ "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j"))))
+ (properties `((upstream-name . "YAPSA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-circlize" ,r-circlize)
+ ("r-complexheatmap" ,r-complexheatmap)
+ ("r-corrplot" ,r-corrplot)
+ ("r-dendextend" ,r-dendextend)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-getoptlong" ,r-getoptlong)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gtrellis" ,r-gtrellis)
+ ("r-keggrest" ,r-keggrest)
+ ("r-lsei" ,r-lsei)
+ ("r-pmcmr" ,r-pmcmr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-somaticsignatures" ,r-somaticsignatures)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/YAPSA/")
+ (synopsis "Yet another package for signature analysis")
+ (description
+ "This package provides functions and routines useful in the analysis of
+somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
+functions to perform a signature analysis with known signatures and a
+signature analysis on @dfn{stratified mutational catalogue} (SMC) are
+provided.")
+ (license license:gpl3)))
+
+(define-public r-gcrma
+ (package
+ (name "r-gcrma")
+ (version "2.54.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "gcrma" version))
+ (sha256
+ (base32
+ "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-affyio" ,r-affyio)
+ ("r-biobase" ,r-biobase)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-biostrings" ,r-biostrings)
+ ("r-xvector" ,r-xvector)))
+ (home-page "https://bioconductor.org/packages/gcrma/")
+ (synopsis "Background adjustment using sequence information")
+ (description
+ "Gcrma adjusts for background intensities in Affymetrix array data which
+include optical noise and @dfn{non-specific binding} (NSB). The main function
+@code{gcrma} converts background adjusted probe intensities to expression
+measures using the same normalization and summarization methods as a
+@dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
+to estimate probe affinity to NSB. The sequence information is summarized in
+a more complex way than the simple GC content. Instead, the base types (A, T,
+G or C) at each position along the probe determine the affinity of each probe.
+The parameters of the position-specific base contributions to the probe
+affinity is estimated in an NSB experiment in which only NSB but no
+gene-specific bidning is expected.")
+ ;; Any version of the LGPL
+ (license license:lgpl2.1+)))
+
+(define-public r-simpleaffy
+ (package
+ (name "r-simpleaffy")
+ (version "2.58.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "simpleaffy" version))
+ (sha256
+ (base32
+ "0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-gcrma" ,r-gcrma)
+ ("r-genefilter" ,r-genefilter)))
+ (home-page "https://bioconductor.org/packages/simpleaffy/")
+ (synopsis "Very simple high level analysis of Affymetrix data")
+ (description
+ "This package provides high level functions for reading Affy @file{.CEL}
+files, phenotypic data, and then computing simple things with it, such as
+t-tests, fold changes and the like. It makes heavy use of the @code{affy}
+library. It also has some basic scatter plot functions and mechanisms for
+generating high resolution journal figures.")
+ (license license:gpl2+)))
+
+(define-public r-yaqcaffy
+ (package
+ (name "r-yaqcaffy")
+ (version "1.42.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "yaqcaffy" version))
+ (sha256
+ (base32
+ "192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-simpleaffy" ,r-simpleaffy)))
+ (home-page "https://bioconductor.org/packages/yaqcaffy/")
+ (synopsis "Affymetrix quality control and reproducibility analysis")
+ (description
+ "This is a package that can be used for quality control of Affymetrix
+GeneChip expression data and reproducibility analysis of human whole genome
+chips with the MAQC reference datasets.")
+ (license license:artistic2.0)))
+
+(define-public r-quantro
+ (package
+ (name "r-quantro")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "quantro" version))
+ (sha256
+ (base32
+ "1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-doparallel" ,r-doparallel)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iterators" ,r-iterators)
+ ("r-minfi" ,r-minfi)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "https://bioconductor.org/packages/quantro/")
+ (synopsis "Test for when to use quantile normalization")
+ (description
+ "This package provides a data-driven test for the assumptions of quantile
+normalization using raw data such as objects that inherit eSets (e.g.
+ExpressionSet, MethylSet). Group level information about each sample (such as
+Tumor / Normal status) must also be provided because the test assesses if
+there are global differences in the distributions between the user-defined
+groups.")
+ (license license:gpl3+)))
+
+(define-public r-yarn
+ (package
+ (name "r-yarn")
+ (version "1.8.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "yarn" version))
+ (sha256
+ (base32
+ "0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biomart" ,r-biomart)
+ ("r-downloader" ,r-downloader)
+ ("r-edger" ,r-edger)
+ ("r-gplots" ,r-gplots)
+ ("r-limma" ,r-limma)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-preprocesscore" ,r-preprocesscore)
+ ("r-quantro" ,r-quantro)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-readr" ,r-readr)))
+ (home-page "https://bioconductor.org/packages/yarn/")
+ (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
+ (description
+ "Expedite large RNA-Seq analyses using a combination of previously
+developed tools. YARN is meant to make it easier for the user in performing
+basic mis-annotation quality control, filtering, and condition-aware
+normalization. YARN leverages many Bioconductor tools and statistical
+techniques to account for the large heterogeneity and sparsity found in very
+large RNA-seq experiments.")
+ (license license:artistic2.0)))
+
+(define-public r-roar
+ (package
+ (name "r-roar")
+ (version "1.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "roar" version))
+ (sha256
+ (base32
+ "15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://github.com/vodkatad/roar/")
+ (synopsis "Identify differential APA usage from RNA-seq alignments")
+ (description
+ "This package provides tools for identifying preferential usage of APA
+sites, comparing two biological conditions, starting from known alternative
+sites and alignments obtained from standard RNA-seq experiments.")
+ (license license:gpl3)))
+
+(define-public r-xbseq
+ (package
+ (name "r-xbseq")
+ (version "1.14.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "XBSeq" version))
+ (sha256
+ (base32
+ "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph"))))
+ (properties `((upstream-name . "XBSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-deseq2" ,r-deseq2)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-locfit" ,r-locfit)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-pracma" ,r-pracma)
+ ("r-roar" ,r-roar)))
+ (home-page "https://github.com/Liuy12/XBSeq")
+ (synopsis "Test for differential expression for RNA-seq data")
+ (description
+ "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
+expression} (DE), where a statistical model was established based on the
+assumption that observed signals are the convolution of true expression
+signals and sequencing noises. The mapped reads in non-exonic regions are
+considered as sequencing noises, which follows a Poisson distribution. Given
+measurable observed signal and background noise from RNA-seq data, true
+expression signals, assuming governed by the negative binomial distribution,
+can be delineated and thus the accurate detection of differential expressed
+genes.")
+ (license license:gpl3+)))
+
+(define-public r-massspecwavelet
+ (package
+ (name "r-massspecwavelet")
+ (version "1.48.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MassSpecWavelet" version))
+ (sha256
+ (base32
+ "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz"))))
+ (properties
+ `((upstream-name . "MassSpecWavelet")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-waveslim" ,r-waveslim)))
+ (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
+ (synopsis "Mass spectrum processing by wavelet-based algorithms")
+ (description
+ "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
+data mainly through the use of wavelet transforms. It supports peak detection
+based on @dfn{Continuous Wavelet Transform} (CWT).")
+ (license license:lgpl2.0+)))
+
+(define-public r-xcms
+ (package
+ (name "r-xcms")
+ (version "3.4.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "xcms" version))
+ (sha256
+ (base32
+ "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-lattice" ,r-lattice)
+ ("r-massspecwavelet" ,r-massspecwavelet)
+ ("r-msnbase" ,r-msnbase)
+ ("r-multtest" ,r-multtest)
+ ("r-mzr" ,r-mzr)
+ ("r-plyr" ,r-plyr)
+ ("r-protgenerics" ,r-protgenerics)
+ ("r-rann" ,r-rann)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-robustbase" ,r-robustbase)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/xcms/")
+ (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
+ (description
+ "This package provides a framework for processing and visualization of
+chromatographically separated and single-spectra mass spectral data. It
+imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
+data for high-throughput, untargeted analyte profiling.")
+ (license license:gpl2+)))
+
+(define-public r-wrench
+ (package
+ (name "r-wrench")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Wrench" version))
+ (sha256
+ (base32
+ "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg"))))
+ (properties `((upstream-name . "Wrench")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-limma" ,r-limma)
+ ("r-locfit" ,r-locfit)
+ ("r-matrixstats" ,r-matrixstats)))
+ (home-page "https://github.com/HCBravoLab/Wrench")
+ (synopsis "Wrench normalization for sparse count data")
+ (description
+ "Wrench is a package for normalization sparse genomic count data, like
+that arising from 16s metagenomic surveys.")
+ (license license:artistic2.0)))
+
+(define-public r-wiggleplotr
+ (package
+ (name "r-wiggleplotr")
+ (version "1.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "wiggleplotr" version))
+ (sha256
+ (base32
+ "12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-assertthat" ,r-assertthat)
+ ("r-cowplot" ,r-cowplot)
+ ("r-dplyr" ,r-dplyr)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-purrr" ,r-purrr)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/wiggleplotr/")
+ (synopsis "Make read coverage plots from BigWig files")
+ (description
+ "This package provides tools to visualize read coverage from sequencing
+experiments together with genomic annotations (genes, transcripts, peaks).
+Introns of long transcripts can be rescaled to a fixed length for better
+visualization of exonic read coverage.")
+ (license license:asl2.0)))
+
+(define-public r-widgettools
+ (package
+ (name "r-widgettools")
+ (version "1.60.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "widgetTools" version))
+ (sha256
+ (base32
+ "0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf"))))
+ (properties `((upstream-name . "widgetTools")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/widgetTools/")
+ (synopsis "Tools for creating interactive tcltk widgets")
+ (description
+ "This packages contains tools to support the construction of tcltk
+widgets in R.")
+ ;; Any version of the LGPL.
+ (license license:lgpl3+)))
+
+(define-public r-webbioc
+ (package
+ (name "r-webbioc")
+ (version "1.54.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "webbioc" version))
+ (sha256
+ (base32
+ "16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi"))))
+ (build-system r-build-system)
+ (inputs
+ `(("netpbm" ,netpbm)
+ ("perl" ,perl)))
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-annaffy" ,r-annaffy)
+ ("r-biobase" ,r-biobase)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-gcrma" ,r-gcrma)
+ ("r-multtest" ,r-multtest)
+ ("r-qvalue" ,r-qvalue)
+ ("r-vsn" ,r-vsn)))
+ (home-page "https://www.bioconductor.org/")
+ (synopsis "Bioconductor web interface")
+ (description
+ "This package provides an integrated web interface for doing microarray
+analysis using several of the Bioconductor packages. It is intended to be
+deployed as a centralized bioinformatics resource for use by many users.
+Currently only Affymetrix oligonucleotide analysis is supported.")
+ (license license:gpl2+)))
+
+(define-public r-zfpkm
+ (package
+ (name "r-zfpkm")
+ (version "1.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "zFPKM" version))
+ (sha256
+ (base32
+ "0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5"))))
+ (properties `((upstream-name . "zFPKM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-checkmate" ,r-checkmate)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-tidyr" ,r-tidyr)))
+ (home-page "https://github.com/ronammar/zFPKM/")
+ (synopsis "Functions to facilitate zFPKM transformations")
+ (description
+ "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
+This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
+24215113).")
+ (license license:gpl3)))
+
+(define-public r-rbowtie2
+ (package
+ (name "r-rbowtie2")
+ (version "1.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rbowtie2" version))
+ (sha256
+ (base32
+ "045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr"))))
+ (properties `((upstream-name . "Rbowtie2")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://bioconductor.org/packages/Rbowtie2/")
+ (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
+ (description
+ "This package provides an R wrapper of the popular @code{bowtie2}
+sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
+rapid adapter trimming, identification, and read merging.")
+ (license license:gpl3+)))
+
+(define-public r-progeny
+ (package
+ (name "r-progeny")
+ (version "1.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "progeny" version))
+ (sha256
+ (base32
+ "02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7"))))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-biobase" ,r-biobase)))
+ (home-page "https://github.com/saezlab/progeny")
+ (synopsis "Pathway responsive gene activity inference")
+ (description
+ "This package provides a function to infer pathway activity from gene
+expression. It contains the linear model inferred in the publication
+\"Perturbation-response genes reveal signaling footprints in cancer gene
+expression\".")
+ (license license:asl2.0)))
+
+(define-public r-arrmnormalization
+ (package
+ (name "r-arrmnormalization")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ARRmNormalization" version))
+ (sha256
+ (base32
+ "09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd"))))
+ (properties
+ `((upstream-name . "ARRmNormalization")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
+ (home-page "https://bioconductor.org/packages/ARRmNormalization/")
+ (synopsis "Adaptive robust regression normalization for methylation data")
+ (description
+ "This is a package to perform the @dfn{Adaptive Robust Regression
+method} (ARRm) for the normalization of methylation data from the Illumina
+Infinium HumanMethylation 450k assay.")
+ (license license:artistic2.0)))
+
+(define-public r-biocfilecache
+ (package
+ (name "r-biocfilecache")
+ (version "1.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocFileCache" version))
+ (sha256
+ (base32
+ "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
+ (properties `((upstream-name . "BiocFileCache")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-curl" ,r-curl)
+ ("r-dbi" ,r-dbi)
+ ("r-dbplyr" ,r-dbplyr)
+ ("r-dplyr" ,r-dplyr)
+ ("r-httr" ,r-httr)
+ ("r-rappdirs" ,r-rappdirs)
+ ("r-rsqlite" ,r-rsqlite)))
+ (home-page "https://bioconductor.org/packages/BiocFileCache/")
+ (synopsis "Manage files across sessions")
+ (description
+ "This package creates a persistent on-disk cache of files that the user
+can add, update, and retrieve. It is useful for managing resources (such as
+custom Txdb objects) that are costly or difficult to create, web resources,
+and data files used across sessions.")
+ (license license:artistic2.0)))
HCoop / jackhill / guix / guix.git / blobdiff