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| author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2023-12-27 11:02:35 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-01-02 10:19:35 +0100 |
| commit | c8e2b85ed1cbb3e17701c838db797ab718d18be0 (patch) | |
| tree | df6230e03d3e937ecd3609cf73630e3b49ccad56 /gnu/packages/bioinformatics.scm | |
| parent | 7593364d70fa81b761c1d9b0269510b21364c6fa (diff) | |
gnu: Add r-stacas.
* gnu/packages/bioinformatics.scm (r-stacas): New variable.
Change-Id: I258a315465ed88b8013d26a36718250c950aa107
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2e4bc876d4..34039b2eb5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1070,6 +1070,42 @@ of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and 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")) |