#: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))
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-lpsymphony
(package
(name "r-lpsymphony")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "lpsymphony" version))
(sha256
(base32
- "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
+ "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
(build-system r-build-system)
(inputs
`(("gfortran" ,gfortran)
(define-public r-ihw
(package
(name "r-ihw")
- (version "1.10.1")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "IHW" version))
(sha256
(base32
- "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
+ "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
(properties `((upstream-name . "IHW")))
(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
(synopsis "Tools for high-throughput metabolomics")
(description
"This package provides tools to analyze and visualize high-throughput
-metabolomics data aquired using chromatography-mass spectrometry. These tools
+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)))
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