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| author | Roel Janssen <roel@gnu.org> | 2021-05-26 13:13:56 +0200 |
|---|---|---|
| committer | Roel Janssen <roel@gnu.org> | 2021-05-26 13:13:56 +0200 |
| commit | 99873359edd7882c776afa326eb23d2d89d87ee2 (patch) | |
| tree | 5a2fb7515f26fa3a1ebaecd62f7c3d7d121a1f35 /gnu/packages/bioconductor.scm | |
| parent | 834f649590db5939e3cd5a18097c7803bd625f82 (diff) | |
gnu: Add r-deepsnv.
* gnu/packages/bioconductor.scm (r-deepsnv): New variable.
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22568353af..7db99fd5ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1408,6 +1408,42 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) +(define-public r-deepsnv + (package + (name "r-deepsnv") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "deepSNV" version)) + (sha256 + (base32 + "1lbvx9liql8fkb4y020kwpgp61vzg67cy640dc4kybglcw9dx6j0")))) + (properties `((upstream-name . "deepSNV"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rhtslib" ,r-rhtslib) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation) + ("r-vgam" ,r-vgam))) + (home-page "https://github.com/gerstung-lab/deepSNV/") + (synopsis "Detection of subclonal SNVs in deep sequencing data") + (description + "This package provides quantitative variant callers for detecting +subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. +The deepSNV algorithm is used for a comparative setup with a control experiment +of the same loci and uses a beta-binomial model and a likelihood ratio test to +discriminate sequencing errors and subclonal SNVs. The shearwater algorithm +computes a Bayes classifier based on a beta-binomial model for variant calling +with multiple samples for precisely estimating model parameters - such as local +error rates and dispersion - and prior knowledge, e.g. from variation data +bases such as COSMIC.") + (license license:gpl3))) + (define-public r-delayedarray (package (name "r-delayedarray") |