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| -rw-r--r-- | gnu/packages/bioconductor.scm | 51 |
1 files changed, 51 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8fe56c4a5b..38a34912ef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8875,6 +8875,57 @@ variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) +;; This package includes files that have been taken from kentutils. Some +;; parts of kentutils are not released under a free license, but this package +;; only uses files that are also found in the free parts of kentutils. +(define-public r-cner + (package + (name "r-cner") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CNEr" version)) + (sha256 + (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c")))) + (properties `((upstream-name . "CNEr"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-go-db" ,r-go-db) + ("r-iranges" ,r-iranges) + ("r-keggrest" ,r-keggrest) + ("r-powerlaw" ,r-powerlaw) + ("r-r-utils" ,r-r-utils) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/ge11232002/CNEr") + (synopsis "CNE Detection and Visualization") + (description + "This package provides tools for large-scale identification and +advanced visualization of sets of conserved noncoding elements.") + ;; For all files in src/ucsc "license is hereby granted for all use - + ;; public, private or commercial"; this includes those files that don't + ;; have a license header, because they are included in the free parts of + ;; the kentutils package. + (license (list license:gpl2 + (license:non-copyleft + "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE"))))) + (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") |