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Change-Id: Ibcf9eaef67398aa00473d29d651c6d32e425d989 --- gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3e7b99ee61..d572980965 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10301,6 +10301,47 @@ (define-public r-sccustomize visualization and analysis of single-cell data using R.") (license license:gpl3+)))) +(define-public r-scgate + (package + (name "r-scgate") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "scGate" version)) + (sha256 + (base32 "0h12d36zjc6fvxbhkxrzbpvw49z9fgyn1jc941q70ajw1yqi2hhh")))) + (properties `((upstream-name . "scGate"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-dplyr + r-ggplot2 + r-ggridges + r-patchwork + r-reshape2 + r-seurat + r-ucell)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/carmonalab/scGate") + (synopsis + "Marker-based cell type purification for single-cell sequencing data") + (description + "This package provides a method to purify a cell type or cell population of +interest from heterogeneous datasets. scGate package automatizes marker-based +purification of specific cell populations, without requiring training data or +reference gene expression profiles. scGate takes as input a gene expression +matrix stored in a Seurat object and a @acronym{GM, gating model}, consisting of +a set of marker genes that define the cell population of interest. It evaluates +the strength of signature marker expression in each cell using the rank-based +method UCell, and then performs @acronym{kNN, k-nearest neighbor} smoothing by +calculating the mean UCell score across neighboring cells. kNN-smoothing aims +at compensating for the large degree of sparsity in scRNAseq data. Finally, a +universal threshold over kNN-smoothed signature scores is applied in binary +decision trees generated from the user-provided gating model, to annotate cells +as either “pure” or “impure”, with respect to the cell population of interest.") + (license license:gpl3))) + (define-public r-markdownhelpers (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe") (revision "1")) base-commit: 0d13d095420861022e68e87ceebd5e037e12a8b3 -- 2.41.0