diff options
| -rw-r--r-- | gnu/packages/bioconductor.scm | 65 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 65 |
2 files changed, 65 insertions, 65 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3dd93e763..55df9bf7d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9308,6 +9308,71 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.") (license license:artistic2.0))) +(define-public r-ggbio + (package + (name "r-ggbio") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggbio" version)) + (sha256 + (base32 + "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; See https://github.com/tengfei/ggbio/issues/117 + ;; This fix will be included in the next release. + (add-after 'unpack 'fix-typo + (lambda _ + (substitute* "R/GGbio-class.R" + (("fechable") "fetchable")) + #t))))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-biovizbase" ,r-biovizbase) + ("r-bsgenome" ,r-bsgenome) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggally" ,r-ggally) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-organismdbi" ,r-organismdbi) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://www.tengfei.name/ggbio/") + (synopsis "Visualization tools for genomic data") + (description + "The ggbio package extends and specializes the grammar of graphics for +biological data. The graphics are designed to answer common scientific +questions, in particular those often asked of high throughput genomics data. +All core Bioconductor data structures are supported, where appropriate. The +package supports detailed views of particular genomic regions, as well as +genome-wide overviews. Supported overviews include ideograms and grand linear +views. High-level plots include sequence fragment length, edge-linked +interval to data view, mismatch pileup, and several splicing summaries.") + (license license:artistic2.0))) + (define-public r-gqtlbase (package (name "r-gqtlbase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bc483e6f13..512abcd8fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10484,71 +10484,6 @@ high-level packages for biological data visualization. This saves development effort and encourages consistency.") (license license:artistic2.0))) -(define-public r-ggbio - (package - (name "r-ggbio") - (version "1.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ggbio" version)) - (sha256 - (base32 - "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; See https://github.com/tengfei/ggbio/issues/117 - ;; This fix will be included in the next release. - (add-after 'unpack 'fix-typo - (lambda _ - (substitute* "R/GGbio-class.R" - (("fechable") "fetchable")) - #t))))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-organismdbi" ,r-organismdbi) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "http://www.tengfei.name/ggbio/") - (synopsis "Visualization tools for genomic data") - (description - "The ggbio package extends and specializes the grammar of graphics for -biological data. The graphics are designed to answer common scientific -questions, in particular those often asked of high throughput genomics data. -All core Bioconductor data structures are supported, where appropriate. The -package supports detailed views of particular genomic regions, as well as -genome-wide overviews. Supported overviews include ideograms and grand linear -views. High-level plots include sequence fragment length, edge-linked -interval to data view, mismatch pileup, and several splicing summaries.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) |