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-rw-r--r--gnu/packages/bioconductor.scm134
1 files changed, 82 insertions, 52 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6ce5c0dc96..bab6b2b64d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -201,14 +201,14 @@ genomes and gene ID formats, largely based on the UCSC table browser.")
(define-public r-hpar
(package
(name "r-hpar")
- (version "1.22.2")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hpar" version))
(sha256
(base32
- "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
+ "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/hpar/")
(synopsis "Human Protein Atlas in R")
@@ -219,23 +219,24 @@ the Human Protein Atlas project.")
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.12.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
+ "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-memoise" ,r-memoise)
- ("r-genomicranges" ,r-genomicranges)
+ `(("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
- ("r-rtracklayer" ,r-rtracklayer)
("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
+ ("r-memoise" ,r-memoise)
+ ("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://bioconductor.org/packages/regioneR/")
(synopsis "Association analysis of genomic regions")
@@ -247,14 +248,14 @@ region sets and other genomic features.")
(define-public r-diffbind
(package
(name "r-diffbind")
- (version "2.8.0")
+ (version "2.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
- "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
+ "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(inputs
@@ -292,14 +293,14 @@ occupancy (overlap) analysis and plotting functions.")
(define-public r-ripseeker
(package
(name "r-ripseeker")
- (version "1.20.0")
+ (version "1.22.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RIPSeeker" version))
(sha256
(base32
- "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
+ "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
(properties `((upstream-name . "RIPSeeker")))
(build-system r-build-system)
(propagated-inputs
@@ -325,14 +326,14 @@ processing to visualization and annotation.")
(define-public r-multtest
(package
(name "r-multtest")
- (version "2.36.0")
+ (version "2.38.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "multtest" version))
(sha256
(base32
- "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
+ "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-survival" ,r-survival)
@@ -363,13 +364,13 @@ expressed genes in DNA microarray experiments.")
(define-public r-graph
(package
(name "r-graph")
- (version "1.58.2")
+ (version "1.60.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "graph" version))
(sha256
(base32
- "07smbb3c30pr5r425g181xsg0rs5jx6x2q6xpwb5dqgicxrz30ga"))))
+ "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
@@ -410,18 +411,19 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
- (version "3.14.2")
+ (version "3.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
- "13rksc65lxxzyw11galh6xzvgzp5ii0gwiwpvrm395v2r17rhwsc"))))
+ "09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocmanager" ,r-biocmanager)
("r-biostrings" ,r-biostrings)
("r-delayedarray" ,r-delayedarray)
("r-go-db" ,r-go-db)
@@ -437,7 +439,6 @@ determining dependencies between variables, code improvement suggestions.")
("r-multtest" ,r-multtest)
("r-rbgl" ,r-rbgl)
("r-graph" ,r-graph)
- ("r-biocinstaller" ,r-biocinstaller)
("r-regioner" ,r-regioner)
("r-dbi" ,r-dbi)
("r-ensembldb" ,r-ensembldb)
@@ -465,12 +466,12 @@ enrichedGO (addGeneIDs).")
(define-public r-marray
(package
(name "r-marray")
- (version "1.58.0")
+ (version "1.60.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "marray" version))
(sha256
- (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
+ (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
(build-system r-build-system)
(propagated-inputs
`(("r-limma" ,r-limma)))
@@ -484,12 +485,12 @@ normalization and quality checking.")
(define-public r-cghbase
(package
(name "r-cghbase")
- (version "1.40.0")
+ (version "1.42.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHbase" version))
(sha256
- (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
+ (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
@@ -504,12 +505,12 @@ the @code{arrayCGH} packages.")
(define-public r-cghcall
(package
(name "r-cghcall")
- (version "2.42.0")
+ (version "2.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "CGHcall" version))
(sha256
- (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
+ (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
@@ -527,12 +528,12 @@ the @code{arrayCGH} packages.")
(define-public r-qdnaseq
(package
(name "r-qdnaseq")
- (version "1.16.0")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "QDNAseq" version))
(sha256
- (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
+ (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
@@ -559,14 +560,14 @@ respectively.")
(define-public r-bayseq
(package
(name "r-bayseq")
- (version "2.14.0")
+ (version "2.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "baySeq" version))
(sha256
(base32
- "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
+ "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
(properties `((upstream-name . "baySeq")))
(build-system r-build-system)
(propagated-inputs
@@ -585,14 +586,14 @@ more complex hypotheses) via empirical Bayesian methods.")
(define-public r-chipcomp
(package
(name "r-chipcomp")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPComp" version))
(sha256
(base32
- "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
+ "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
(properties `((upstream-name . "ChIPComp")))
(build-system r-build-system)
(propagated-inputs
@@ -619,14 +620,14 @@ datasets.")
(define-public r-riboprofiling
(package
(name "r-riboprofiling")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RiboProfiling" version))
(sha256
(base32
- "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
+ "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
(properties `((upstream-name . "RiboProfiling")))
(build-system r-build-system)
(propagated-inputs
@@ -658,14 +659,14 @@ assessment, principal component analysis on codon coverage.")
(define-public r-riboseqr
(package
(name "r-riboseqr")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "riboSeqR" version))
(sha256
(base32
- "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
+ "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
(properties `((upstream-name . "riboSeqR")))
(build-system r-build-system)
(propagated-inputs
@@ -686,14 +687,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
(define-public r-interactionset
(package
(name "r-interactionset")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "InteractionSet" version))
(sha256
(base32
- "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
+ "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
(properties
`((upstream-name . "InteractionSet")))
(build-system r-build-system)
@@ -718,14 +719,14 @@ experiments.")
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
+ "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
@@ -757,14 +758,14 @@ information and producing various plots and statistics.")
(define-public r-ctc
(package
(name "r-ctc")
- (version "1.54.0")
+ (version "1.56.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ctc" version))
(sha256
(base32
- "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9"))))
+ "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
(build-system r-build-system)
(propagated-inputs `(("r-amap" ,r-amap)))
(home-page "https://bioconductor.org/packages/ctc/")
@@ -777,14 +778,14 @@ trees and clusters to other programs.")
(define-public r-goseq
(package
(name "r-goseq")
- (version "1.32.0")
+ (version "1.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "goseq" version))
(sha256
(base32
- "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l"))))
+ "1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -803,14 +804,14 @@ defined categories which are over/under represented in RNA-seq data.")
(define-public r-glimma
(package
(name "r-glimma")
- (version "1.8.2")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Glimma" version))
(sha256
(base32
- "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s"))))
+ "0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947"))))
(properties `((upstream-name . "Glimma")))
(build-system r-build-system)
(propagated-inputs
@@ -830,14 +831,14 @@ information.")
(define-public r-rots
(package
(name "r-rots")
- (version "1.8.0")
+ (version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ROTS" version))
(sha256
(base32
- "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3"))))
+ "137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5"))))
(properties `((upstream-name . "ROTS")))
(build-system r-build-system)
(propagated-inputs
@@ -854,14 +855,14 @@ in omics data.")
(define-public r-inspect
(package
(name "r-inspect")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "INSPEcT" version))
(sha256
(base32
- "1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p"))))
+ "0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2"))))
(properties `((upstream-name . "INSPEcT")))
(build-system r-build-system)
(propagated-inputs
@@ -890,14 +891,14 @@ modeling the rates that determines changes in mature mRNA levels.")
(define-public r-dnabarcodes
(package
(name "r-dnabarcodes")
- (version "1.10.0")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DNABarcodes" version))
(sha256
(base32
- "0xhna7f0kr7pp2hqwara5i57m9mdr65shflfxiyw6yy3g90pgb5x"))))
+ "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
(properties `((upstream-name . "DNABarcodes")))
(build-system r-build-system)
(propagated-inputs
@@ -917,14 +918,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
(define-public r-ruvseq
(package
(name "r-ruvseq")
- (version "1.14.0")
+ (version "1.16.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RUVSeq" version))
(sha256
(base32
- "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj"))))
+ "0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m"))))
(properties `((upstream-name . "RUVSeq")))
(build-system r-build-system)
(propagated-inputs
@@ -939,3 +940,32 @@ demultiplexed, i.e. assigned to their original reference barcode.")
of Risso et al. (2014) for the normalization of RNA-Seq read counts between
samples.")
(license license:artistic2.0)))
+
+(define-public r-biocneighbors
+ (package
+ (name "r-biocneighbors")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocNeighbors" version))
+ (sha256
+ (base32
+ "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
+ (properties `((upstream-name . "BiocNeighbors")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppannoy" ,r-rcppannoy)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/BiocNeighbors")
+ (synopsis "Nearest Neighbor Detection for Bioconductor packages")
+ (description
+ "This package implements exact and approximate methods for nearest
+neighbor detection, in a framework that allows them to be easily switched
+within Bioconductor packages or workflows. The exact algorithm is implemented
+using pre-clustering with the k-means algorithm. Functions are also provided
+to search for all neighbors within a given distance. Parallelization is
+achieved for all methods using the BiocParallel framework.")
+ (license license:gpl3)))