gnu: r-chipseeker: Move out of experiment section.
* gnu/packages/bioconductor.scm (r-chipseeker): Move the package from the "experiment" section to the section for regular Bioconductor packages.master
Ricardo Wurmus
parent
a6e7afd4d5
commit
ec543ba672
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@ -1080,54 +1080,6 @@ from Illumina 450k methylation arrays.")
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chromstaR package.")
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(license license:gpl3)))
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(define-public r-chipseeker
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(package
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(name "r-chipseeker")
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(version "1.26.2")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "ChIPseeker" version))
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(sha256
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(base32
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"1r197qwsriap6s6nb2p9j3521pjs2f0lgyzvppvlxj1531sa6g6z"))))
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(build-system r-build-system)
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(inputs
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`(("r-knitr" ,r-knitr)))
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(propagated-inputs
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`(("r-annotationdbi" ,r-annotationdbi)
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("r-biocgenerics" ,r-biocgenerics)
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("r-boot" ,r-boot)
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("r-enrichplot" ,r-enrichplot)
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("r-iranges" ,r-iranges)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicranges" ,r-genomicranges)
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("r-genomicfeatures" ,r-genomicfeatures)
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("r-ggplot2" ,r-ggplot2)
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("r-gplots" ,r-gplots)
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("r-gtools" ,r-gtools)
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("r-dplyr" ,r-dplyr)
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("r-plotrix" ,r-plotrix)
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("r-dplyr" ,r-dplyr)
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("r-magrittr" ,r-magrittr)
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("r-rcolorbrewer" ,r-rcolorbrewer)
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("r-rtracklayer" ,r-rtracklayer)
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("r-s4vectors" ,r-s4vectors)
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("r-txdb-hsapiens-ucsc-hg19-knowngene"
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,r-txdb-hsapiens-ucsc-hg19-knowngene)))
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(home-page "https://www.bioconductor.org/packages/ChIPseeker/")
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(synopsis
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"ChIPseeker for ChIP peak Annotation, Comparison, and Visualization")
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(description "This package implements functions to retrieve the nearest
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genes around the peak, annotate genomic region of the peak, statstical methods
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for estimate the significance of overlap among ChIP peak data sets, and
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incorporate GEO database for user to compare the own dataset with those
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deposited in database. The comparison can be used to infer cooperative
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regulation and thus can be used to generate hypotheses. Several visualization
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functions are implemented to summarize the coverage of the peak experiment,
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average profile and heatmap of peaks binding to TSS regions, genomic
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annotation, distance to TSS, and overlap of peaks or genes.")
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(license license:artistic2.0)))
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(define-public r-copyhelper
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(package
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(name "r-copyhelper")
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@ -2415,6 +2367,53 @@ genome data packages and support for efficient SNP representation.")
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analysis.")
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(license license:artistic2.0)))
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(define-public r-chipseeker
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(package
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(name "r-chipseeker")
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(version "1.26.2")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "ChIPseeker" version))
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(sha256
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(base32
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"1r197qwsriap6s6nb2p9j3521pjs2f0lgyzvppvlxj1531sa6g6z"))))
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(build-system r-build-system)
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(inputs
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`(("r-knitr" ,r-knitr)))
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(propagated-inputs
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`(("r-annotationdbi" ,r-annotationdbi)
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("r-biocgenerics" ,r-biocgenerics)
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("r-boot" ,r-boot)
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("r-enrichplot" ,r-enrichplot)
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("r-iranges" ,r-iranges)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicranges" ,r-genomicranges)
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("r-genomicfeatures" ,r-genomicfeatures)
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("r-ggplot2" ,r-ggplot2)
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("r-gplots" ,r-gplots)
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("r-gtools" ,r-gtools)
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("r-dplyr" ,r-dplyr)
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("r-plotrix" ,r-plotrix)
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("r-dplyr" ,r-dplyr)
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("r-magrittr" ,r-magrittr)
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("r-rcolorbrewer" ,r-rcolorbrewer)
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("r-rtracklayer" ,r-rtracklayer)
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("r-s4vectors" ,r-s4vectors)
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("r-txdb-hsapiens-ucsc-hg19-knowngene"
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,r-txdb-hsapiens-ucsc-hg19-knowngene)))
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(home-page "https://www.bioconductor.org/packages/ChIPseeker/")
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(synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
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(description "This package implements functions to retrieve the nearest
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genes around the peak, annotate genomic region of the peak, statstical methods
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for estimate the significance of overlap among ChIP peak data sets, and
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incorporate GEO database for user to compare the own dataset with those
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deposited in database. The comparison can be used to infer cooperative
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regulation and thus can be used to generate hypotheses. Several visualization
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functions are implemented to summarize the coverage of the peak experiment,
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average profile and heatmap of peaks binding to TSS regions, genomic
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annotation, distance to TSS, and overlap of peaks or genes.")
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(license license:artistic2.0)))
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(define-public r-chipseq
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(package
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(name "r-chipseq")
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