diff options
| -rw-r--r-- | gnu/packages/bioconductor.scm | 48 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
2 files changed, 48 insertions, 48 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8cf8b43ed4..b90e315267 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -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") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1396631591..cc6e1b1594 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |