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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: 0.6.2
Depends: R (≥ 4.3.0)
Imports: RcppML, Matrix, stats, methods, utils, Seurat (≥ 4.3.0), cluster, lsa, irlba, pheatmap, dendextend, viridis
Suggests: knitr, rmarkdown, fgsea, msigdbr
Published: 2024-11-12
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 (source)

Downloads:

Package source: GeneNMF_0.6.2.tar.gz
Windows binaries: r-devel: GeneNMF_0.6.0.zip, r-release: GeneNMF_0.6.0.zip, r-oldrel: GeneNMF_0.6.0.zip
macOS binaries: r-release (arm64): GeneNMF_0.6.0.tgz, r-oldrel (arm64): GeneNMF_0.6.0.tgz, r-release (x86_64): GeneNMF_0.6.0.tgz, r-oldrel (x86_64): GeneNMF_0.6.0.tgz
Old sources: GeneNMF archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.