diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 46 |
1 files changed, 46 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 407d3ee93b..baa1f71524 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5459,3 +5459,49 @@ with multiple R processes supported by the package @code{parallel}.") "This package provides methods for working with Illumina arrays using the @code{gdsfmt} package.") (license license:gpl3))) + +(define-public r-wavcluster + (package + (name "r-wavcluster") + (version "2.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "wavClusteR" version)) + (sha256 + (base32 + "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2")))) + (properties `((upstream-name . "wavClusteR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-foreach" ,r-foreach) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-mclust" ,r-mclust) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-seqinr" ,r-seqinr) + ("r-stringr" ,r-stringr) + ("r-wmtsa" ,r-wmtsa))) + (home-page "https://bioconductor.org/packages/wavClusteR/") + (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") + (description + "This package provides an integrated pipeline for the analysis of +PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from +sequencing errors, SNPs and additional non-experimental sources by a non- +parametric mixture model. The protein binding sites (clusters) are then +resolved at high resolution and cluster statistics are estimated using a +rigorous Bayesian framework. Post-processing of the results, data export for +UCSC genome browser visualization and motif search analysis are provided. In +addition, the package allows to integrate RNA-Seq data to estimate the False +Discovery Rate of cluster detection. Key functions support parallel multicore +computing. While wavClusteR was designed for PAR-CLIP data analysis, it can +be applied to the analysis of other NGS data obtained from experimental +procedures that induce nucleotide substitutions (e.g. BisSeq).") + (license license:gpl2))) |