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author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2023-12-27 11:02:34 +0100 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2024-01-02 10:19:29 +0100 |
commit | 7593364d70fa81b761c1d9b0269510b21364c6fa (patch) | |
tree | e582445021c4257528570b92d5ece6cadfcc4f89 /gnu | |
parent | f2102cb5b9239be2ed2023b908b726af542e0124 (diff) |
gnu: Add r-scgate.
* gnu/packages/bioconductor.scm (r-scgate): New variable.
Change-Id: I441bbea5a68882f5f619dea72abdf84619c9d02f
Diffstat (limited to 'gnu')
-rw-r--r-- | gnu/packages/bioconductor.scm | 43 |
1 files changed, 43 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 316aa20026..427fa4ebfe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10315,6 +10315,49 @@ comprehensive scDblFinder method.") (license license:gpl3))) ;; This is a CRAN package, but it depends on packages from Bioconductor. +(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))) + +;; This is a CRAN package, but it depends on packages from Bioconductor. (define-public r-scistreer (package (name "r-scistreer") |