GeneNMF: Non-Negative Matrix Factorization for Single-Cell Omics

A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.

Version: 0.4.0
Depends: R (≥ 4.3.0)
Imports: RcppML, NMF, stats, Seurat (≥ 4.3.0), cluster, pheatmap, viridis
Suggests: knitr, rmarkdown, fgsea, dplyr, msigdbr
Published: 2024-02-29
Author: Massimo Andreatta ORCID iD [aut, cre], Santiago Carmona ORCID iD [aut]
Maintainer: Massimo Andreatta <massimo.andreatta at unil.ch>
BugReports: https://github.com/carmonalab/GeneNMF/issues
License: GPL-3
URL: https://github.com/carmonalab/GeneNMF
NeedsCompilation: no
Materials: README NEWS
CRAN checks: GeneNMF results

Documentation:

Reference manual: GeneNMF.pdf
Vignettes: Index of GeneNMF vignettes

Downloads:

Package source: GeneNMF_0.4.0.tar.gz
Windows binaries: r-prerel: GeneNMF_0.4.0.zip, r-release: GeneNMF_0.4.0.zip, r-oldrel: not available
macOS binaries: r-prerel (arm64): GeneNMF_0.4.0.tgz, r-release (arm64): GeneNMF_0.4.0.tgz, r-oldrel (arm64): not available, r-prerel (x86_64): GeneNMF_0.4.0.tgz, r-release (x86_64): GeneNMF_0.4.0.tgz

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