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gnu: r-chipseeker: Move out of experiment section.

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* gnu/packages/bioconductor.scm (r-chipseeker): Move the package from the
"experiment" section to the section for regular Bioconductor packages.
This commit is contained in:
Ricardo Wurmus 2021-05-31 15:54:41 +02:00
parent a6e7afd4d5
commit ec543ba672
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GPG key ID: 197A5888235FACAC
1 changed files with 47 additions and 48 deletions
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95
gnu/packages/bioconductor.scm
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@ -1080,54 +1080,6 @@ (define-public r-chromstardata
chromstaR package.")
(license license:gpl3)))
(define-public r-chipseeker
(package
(name "r-chipseeker")
(version "1.26.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ChIPseeker" version))
(sha256
(base32
"1r197qwsriap6s6nb2p9j3521pjs2f0lgyzvppvlxj1531sa6g6z"))))
(build-system r-build-system)
(inputs
`(("r-knitr" ,r-knitr)))
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biocgenerics" ,r-biocgenerics)
("r-boot" ,r-boot)
("r-enrichplot" ,r-enrichplot)
("r-iranges" ,r-iranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-genomicfeatures" ,r-genomicfeatures)
("r-ggplot2" ,r-ggplot2)
("r-gplots" ,r-gplots)
("r-gtools" ,r-gtools)
("r-dplyr" ,r-dplyr)
("r-plotrix" ,r-plotrix)
("r-dplyr" ,r-dplyr)
("r-magrittr" ,r-magrittr)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-txdb-hsapiens-ucsc-hg19-knowngene"
,r-txdb-hsapiens-ucsc-hg19-knowngene)))
(home-page "https://www.bioconductor.org/packages/ChIPseeker/")
(synopsis
"ChIPseeker for ChIP peak Annotation, Comparison, and Visualization")
(description "This package implements functions to retrieve the nearest
genes around the peak, annotate genomic region of the peak, statstical methods
for estimate the significance of overlap among ChIP peak data sets, and
incorporate GEO database for user to compare the own dataset with those
deposited in database. The comparison can be used to infer cooperative
regulation and thus can be used to generate hypotheses. Several visualization
functions are implemented to summarize the coverage of the peak experiment,
average profile and heatmap of peaks binding to TSS regions, genomic
annotation, distance to TSS, and overlap of peaks or genes.")
(license license:artistic2.0)))
(define-public r-copyhelper
(package
(name "r-copyhelper")
@ -2415,6 +2367,53 @@ (define-public r-category
analysis.")
(license license:artistic2.0)))
(define-public r-chipseeker
(package
(name "r-chipseeker")
(version "1.26.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ChIPseeker" version))
(sha256
(base32
"1r197qwsriap6s6nb2p9j3521pjs2f0lgyzvppvlxj1531sa6g6z"))))
(build-system r-build-system)
(inputs
`(("r-knitr" ,r-knitr)))
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biocgenerics" ,r-biocgenerics)
("r-boot" ,r-boot)
("r-enrichplot" ,r-enrichplot)
("r-iranges" ,r-iranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-genomicfeatures" ,r-genomicfeatures)
("r-ggplot2" ,r-ggplot2)
("r-gplots" ,r-gplots)
("r-gtools" ,r-gtools)
("r-dplyr" ,r-dplyr)
("r-plotrix" ,r-plotrix)
("r-dplyr" ,r-dplyr)
("r-magrittr" ,r-magrittr)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-txdb-hsapiens-ucsc-hg19-knowngene"
,r-txdb-hsapiens-ucsc-hg19-knowngene)))
(home-page "https://www.bioconductor.org/packages/ChIPseeker/")
(synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
(description "This package implements functions to retrieve the nearest
genes around the peak, annotate genomic region of the peak, statstical methods
for estimate the significance of overlap among ChIP peak data sets, and
incorporate GEO database for user to compare the own dataset with those
deposited in database. The comparison can be used to infer cooperative
regulation and thus can be used to generate hypotheses. Several visualization
functions are implemented to summarize the coverage of the peak experiment,
average profile and heatmap of peaks binding to TSS regions, genomic
annotation, distance to TSS, and overlap of peaks or genes.")
(license license:artistic2.0)))
(define-public r-chipseq
(package
(name "r-chipseq")