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gnu: r-genomation: Move to (gnu packages bioconductor). 

* gnu/packages/bioinformatics.scm (r-genomation): Move from here...
* gnu/packages/bioconductor.scm (r-genomation): ...to here.
master
zimoun 2021-05-21 22:25:44 +02:00 committed by Ricardo Wurmus
parent f3b50aa4fd
commit f8fe5497c7
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2 changed files with 48 additions and 48 deletions
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48
gnu/packages/bioconductor.scm
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@ -2304,6 +2304,54 @@ CAGE.")
high-throughput sequencing experiments.")
(license license:artistic2.0)))
(define-public r-genomation
(package
(name "r-genomation")
(version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "genomation" version))
(sha256
(base32
"1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
("r-data-table" ,r-data-table)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicalignments" ,r-genomicalignments)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-gridbase" ,r-gridbase)
("r-impute" ,r-impute)
("r-iranges" ,r-iranges)
("r-matrixstats" ,r-matrixstats)
("r-plotrix" ,r-plotrix)
("r-plyr" ,r-plyr)
("r-rcpp" ,r-rcpp)
("r-readr" ,r-readr)
("r-reshape2" ,r-reshape2)
("r-rsamtools" ,r-rsamtools)
("r-rtracklayer" ,r-rtracklayer)
("r-runit" ,r-runit)
("r-s4vectors" ,r-s4vectors)
("r-seqpattern" ,r-seqpattern)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioinformatics.mdc-berlin.de/genomation/")
(synopsis "Summary, annotation and visualization of genomic data")
(description
"This package provides a package for summary and annotation of genomic
intervals. Users can visualize and quantify genomic intervals over
pre-defined functional regions, such as promoters, exons, introns, etc. The
genomic intervals represent regions with a defined chromosome position, which
may be associated with a score, such as aligned reads from HT-seq experiments,
TF binding sites, methylation scores, etc. The package can use any tabular
genomic feature data as long as it has minimal information on the locations of
genomic intervals. In addition, it can use BAM or BigWig files as input.")
(license license:artistic2.0)))
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")

48
gnu/packages/bioinformatics.scm
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@ -8023,54 +8023,6 @@ used to obtain robust estimates of the predominant fragment length or
characteristic tag shift values in these assays.")
(license license:bsd-3)))
(define-public r-genomation
(package
(name "r-genomation")
(version "1.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "genomation" version))
(sha256
(base32
"1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
("r-bsgenome" ,r-bsgenome)
("r-data-table" ,r-data-table)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicalignments" ,r-genomicalignments)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-gridbase" ,r-gridbase)
("r-impute" ,r-impute)
("r-iranges" ,r-iranges)
("r-matrixstats" ,r-matrixstats)
("r-plotrix" ,r-plotrix)
("r-plyr" ,r-plyr)
("r-rcpp" ,r-rcpp)
("r-readr" ,r-readr)
("r-reshape2" ,r-reshape2)
("r-rsamtools" ,r-rsamtools)
("r-rtracklayer" ,r-rtracklayer)
("r-runit" ,r-runit)
("r-s4vectors" ,r-s4vectors)
("r-seqpattern" ,r-seqpattern)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://bioinformatics.mdc-berlin.de/genomation/")
(synopsis "Summary, annotation and visualization of genomic data")
(description
"This package provides a package for summary and annotation of genomic
intervals. Users can visualize and quantify genomic intervals over
pre-defined functional regions, such as promoters, exons, introns, etc. The
genomic intervals represent regions with a defined chromosome position, which
may be associated with a score, such as aligned reads from HT-seq experiments,
TF binding sites, methylation scores, etc. The package can use any tabular
genomic feature data as long as it has minimal information on the locations of
genomic intervals. In addition, it can use BAM or BigWig files as input.")
(license license:artistic2.0)))
(define-public r-genomationdata
(package
(name "r-genomationdata")