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Change-Id: I258a315465ed88b8013d26a36718250c950aa107 --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d572980965..d736abe07e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1069,6 +1069,42 @@ (define-public r-singlet similar.") (license license:gpl2+)))) +(define-public r-stacas + (package + (name "r-stacas") + (version "2.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/carmonalab/STACAS") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "13i0h5i6vlbrb8ndq9gr81560z9d74b2c7m3rjfzls01irjza9hm")))) + (properties `((upstream-name . "STACAS"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocneighbors + r-biocparallel + r-ggplot2 + r-ggridges + r-pbapply + r-r-utils + r-seurat)) + (home-page "https://github.com/carmonalab/STACAS") + (synopsis "Sub-type anchoring correction for alignment in Seurat") + (description + "This package implements methods for batch correction and integration of +scRNA-seq datasets, based on the Seurat anchor-based integration framework. In +particular, STACAS is optimized for the integration of heterogenous datasets with +only limited overlap between cell sub-types (e.g. TIL sets of CD8 from tumor with +CD8/CD4 T cells from lymphnode), for which the default Seurat alignment methods +would tend to over-correct biological differences. The 2.0 version of the package +allows the users to incorporate explicit information about cell-types in order +to assist the integration process.") + (license license:gpl3))) + (define-public r-stringendo (let ((commit "15594b1bba11048a812874bafec0eea1dcc8618a") (revision "1"))