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| -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 815efa1ae0..151d74d25c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14556,6 +14556,52 @@ ensemble machine learning for the estimation of nuisance functions.") visualizing bisulfite sequencing data.") (license license:artistic2.0))) +(define-public r-dmrseq + (package + (name "r-dmrseq") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "dmrseq" version)) + (sha256 + (base32 + "1jbbjifjsnk9261wqmdwkbzj1w52g6vaanpk4w816ri0fap587m4")))) + (properties `((upstream-name . "dmrseq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-annotatr" ,r-annotatr) + ("r-biocparallel" ,r-biocparallel) + ("r-bsseq" ,r-bsseq) + ("r-bumphunter" ,r-bumphunter) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-locfit" ,r-locfit) + ("r-matrixstats" ,r-matrixstats) + ("r-nlme" ,r-nlme) + ("r-outliers" ,r-outliers) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/dmrseq") + (synopsis "Detection and inference of differentially methylated regions") + (description + "This package implements an approach for scanning the genome to detect +and perform accurate inference on differentially methylated regions from Whole +Genome Bisulfite Sequencing data. The method is based on comparing detected +regions to a pooled null distribution, that can be implemented even when as +few as two samples per population are available. Region-level statistics are +obtained by fitting a @dfn{generalized least squares} (GLS) regression model +with a nested autoregressive correlated error structure for the effect of +interest on transformed methylation proportions.") + (license license:expat))) + (define-public r-tximeta (package (name "r-tximeta") |