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Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ca0521578..b58c5bc11f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5013,6 +5013,51 @@ Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.") (license license:gpl2))) +(define-public r-tradeseq + (package + (name "r-tradeseq") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tradeSeq" version)) + (sha256 + (base32 + "1ncmvn9kaksismvsjs042xsp8bfq1xnm0ds87dwpk95bnpj96a89")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocparallel" ,r-biocparallel) + ("r-clusterexperiment" ,r-clusterexperiment) + ("r-dplyr" ,r-dplyr) + ("r-edger" ,r-edger) + ("r-ggplot2" ,r-ggplot2) + ("r-igraph" ,r-igraph) + ("r-magrittr" ,r-magrittr) + ("r-mgcv" ,r-mgcv) + ("r-monocle" ,r-monocle) + ("r-pbapply" ,r-pbapply) + ("r-princurve" ,r-princurve) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-slingshot" ,r-slingshot) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://statomics.github.io/tradeSeq/index.html") + (synopsis "Trajectory-based differential expression analysis") + (description + "This package provides a flexible method for fitting regression models that +can be used to find genes that are differentially expressed along one or +multiple lineages in a trajectory. Based on the fitted models, it uses a +variety of tests suited to answer different questions of interest, e.g. the +discovery of genes for which expression is associated with pseudotime, or which +are differentially expressed (in a specific region) along the trajectory. It +fits a negative binomial generalized additive model (GAM) for each gene, and +performs inference on the parameters of the GAM.") + (license license:expat))) + (define-public r-triform (package (name "r-triform") |