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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-10-14 18:22:46 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-10-14 18:22:46 +0200 |
| commit | b06cdce923d6b8b40c1238cb1a2b9db277d3394e (patch) | |
| tree | b1f595e587020cf9aff6dd390610ecce2ce20531 | |
| parent | 40be965e28062ab37ab7c7ed6647600fa8671ed0 (diff) | |
| download | patches-b06cdce923d6b8b40c1238cb1a2b9db277d3394e.tar patches-b06cdce923d6b8b40c1238cb1a2b9db277d3394e.tar.gz | |
gnu: Add r-velocyto.
* gnu/packages/bioinformatics.scm (r-velocyto): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a573ef682f..12c30236cb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15260,3 +15260,47 @@ and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.") (license license:expat))) + +(define-public r-velocyto + (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350") + (revision "1")) + (package + (name "r-velocyto") + (version (git-version "0.6" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/velocyto-team/velocyto.R.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16wqf70j7rd7pay2q513iyz12i8n9vrpg1bisah4lddbcpx5dz1n")))) + (build-system r-build-system) + (inputs + `(("boost" ,boost))) + (propagated-inputs + `(("r-hdf5r" ,r-hdf5r) + ("r-mass" ,r-mass) + ("r-mgcv" ,r-mgcv) + ("r-pcamethods" ,r-pcamethods) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ;; Suggested packages + ("r-rtsne" ,r-rtsne) + ("r-cluster" ,r-cluster) + ("r-abind" ,r-abind) + ("r-h5" ,r-h5) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicalignments" ,r-genomicalignments) + ("r-rsamtools" ,r-rsamtools) + ("r-edger" ,r-edger) + ("r-igraph" ,r-igraph))) + (home-page "http://velocyto.org") + (synopsis "RNA velocity estimation in R") + (description + "This package provides basic routines for estimation of gene-specific +transcriptional derivatives and visualization of the resulting velocity +patterns.") + (license license:gpl3)))) |