summaryrefslogtreecommitdiff
path: root/gnu/packages/bioconductor.scm
diff options
context:
space:
mode:
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r--gnu/packages/bioconductor.scm77
1 files changed, 53 insertions, 24 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a8ed2707ac..b191c8b4ae 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1396,14 +1396,14 @@ the Human Protein Atlas project.")
(define-public r-regioner
(package
(name "r-regioner")
- (version "1.20.0")
+ (version "1.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
- "10i21gxv0n7lrflhj5ja672xjizy1i4y4iq3pmjgbf0dpy1lxsih"))))
+ "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
@@ -1587,7 +1587,7 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
("r-reshape2" ,r-reshape2)))
(native-inputs
`(("r-knitr" ,r-knitr)))
- (home-page "http://github.com/jdstorey/qvalue")
+ (home-page "https://github.com/StoreyLab/qvalue")
(synopsis "Q-value estimation for false discovery rate control")
(description
"This package takes a list of p-values resulting from the simultaneous
@@ -2934,7 +2934,7 @@ qPCR data, but could be used with other types as well.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/cole-trapnell-lab/monocle3.git")
+ (url "https://github.com/cole-trapnell-lab/monocle3")
(commit version)))
(file-name (git-file-name name version))
(sha256
@@ -5119,14 +5119,14 @@ that arising from 16s metagenomic surveys.")
(define-public r-wiggleplotr
(package
(name "r-wiggleplotr")
- (version "1.12.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "wiggleplotr" version))
(sha256
(base32
- "15l8f7ls2mwhsw68sr1k4r19hmdzjriibr5hpnfbanzj5x6yhdjq"))))
+ "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -5781,14 +5781,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "2.2.2")
+ (version "2.2.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "1wgilpaw70dwg0zilx5i1pmi4j8wri6wi2ha1d3bapfhlwc6igml"))))
+ "0yznfqgp5cbz68n3rrfvm752267da16kl538zdrb1g1aw9zdfqc6"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))
@@ -6248,14 +6248,14 @@ sequential way to mimic the manual gating strategy.")
(define-public r-cytoml
(package
(name "r-cytoml")
- (version "2.0.0")
+ (version "2.0.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CytoML" version))
(sha256
(base32
- "0zpq2j4y9i5lls1kj2w4spl8qjp3076idsr2a2rjvy1fykzlp01q"))))
+ "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n"))))
(properties `((upstream-name . "CytoML")))
(build-system r-build-system)
(inputs
@@ -6286,6 +6286,7 @@ sequential way to mimic the manual gating strategy.")
("r-runit" ,r-runit)
("r-tibble" ,r-tibble)
("r-xml" ,r-xml)
+ ("r-xml2" ,r-xml2)
("r-yaml" ,r-yaml)))
(native-inputs
`(("r-knitr" ,r-knitr)))
@@ -6373,14 +6374,14 @@ delete entire rows with missing data.")
(define-public r-depecher
(package
(name "r-depecher")
- (version "1.4.0")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DepecheR" version))
(sha256
(base32
- "0nmx04qybzf6nhfngmdxwpbbz9x32v34mbnpg8jq7a2cgchzsj9s"))))
+ "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v"))))
(properties `((upstream-name . "DepecheR")))
(build-system r-build-system)
(propagated-inputs
@@ -6455,14 +6456,14 @@ genes in the gene-set that are ranked above the leading edge).")
(define-public r-cicero
(package
(name "r-cicero")
- (version "1.6.0")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cicero" version))
(sha256
(base32
- "0n78lf5hz6zzl550dbf4imis43pv91zicfff8y4lspckljhz9z75"))))
+ "0nf9yqg5krj26n4n82iyx3rsr84d46b17i9zfk35sh12l4xssbii"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -6482,6 +6483,7 @@ genes in the gene-set that are ranked above the leading edge).")
("r-plyr" ,r-plyr)
("r-reshape2" ,r-reshape2)
("r-s4vectors" ,r-s4vectors)
+ ("r-stringi" ,r-stringi)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
@@ -6507,7 +6509,7 @@ accessibility data.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/cole-trapnell-lab/cicero-release.git")
+ (url "https://github.com/cole-trapnell-lab/cicero-release")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -6528,7 +6530,7 @@ accessibility data.")
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/aertslab/cisTopic.git")
+ (url "https://github.com/aertslab/cisTopic")
(commit commit)))
(file-name (git-file-name name version))
(sha256
@@ -6673,14 +6675,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
(define-public r-gdsfmt
(package
(name "r-gdsfmt")
- (version "1.24.0")
+ (version "1.24.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gdsfmt" version))
(sha256
(base32
- "00hggma0i15w03xi9jr02v2593jbqkcxyfcvpp7mdzrshn99m9p6"))
+ "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67"))
(modules '((guix build utils)))
;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
;; them and link with system libraries instead.
@@ -7046,14 +7048,14 @@ arrays based on fast wavelet-based functional models.")
(define-public r-variancepartition
(package
(name "r-variancepartition")
- (version "1.18.0")
+ (version "1.18.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "variancePartition" version))
(sha256
(base32
- "1rn655qq7dshbk1dd41n7y2hfz8498jxd2j4rk7p8hrikd3s32dm"))))
+ "19bhkb8vd44m3nkznw075fx3y2p3a1bsazbhcfiqw9n4190k9bgv"))))
(properties
`((upstream-name . "variancePartition")))
(build-system r-build-system)
@@ -7185,21 +7187,20 @@ using whole genome sequencing data.")
(define-public r-activepathways
(package
(name "r-activepathways")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ActivePathways" version))
(sha256
(base32
- "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20"))))
+ "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
(properties
`((upstream-name . "ActivePathways")))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
- ("r-ggplot2" ,r-ggplot2)
- ("r-metap" ,r-metap)))
+ ("r-ggplot2" ,r-ggplot2)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/ActivePathways/")
@@ -8087,3 +8088,31 @@ metrics, such as the elbow method and Horn's parallel analysis, which has
relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
dimensional mass cytometry data.")
(license license:gpl3)))
+
+(define-public r-rgreat
+ (package
+ (name "r-rgreat")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rGREAT" version))
+ (sha256
+ (base32
+ "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v"))))
+ (properties `((upstream-name . "rGREAT")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genomicranges" ,r-genomicranges)
+ ("r-getoptlong" ,r-getoptlong)
+ ("r-iranges" ,r-iranges)
+ ("r-rcurl" ,r-rcurl)
+ ("r-rjson" ,r-rjson)))
+ (native-inputs `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/jokergoo/rGREAT")
+ (synopsis "Client for GREAT analysis")
+ (description
+ "This package makes GREAT (Genomic Regions Enrichment of Annotations
+Tool) analysis automatic by constructing a HTTP POST request according to
+user's input and automatically retrieving results from GREAT web server.")
+ (license license:expat)))
generated by cgit v1.2.3 (git 2.45.2) at 2024-08-15 20:51:52 +0000