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: | 0.9.2 |
| Depends: | R (≥ 4.3.0) |
| Imports: | RcppML, Matrix, stats, methods, utils, Seurat (≥ 4.3.0), cluster, lsa, irlba, pheatmap, dendextend, viridis, colorspace |
| Suggests: | knitr, rmarkdown, fgsea, msigdbr |
| Published: | 2025-09-11 |
| DOI: | 10.32614/CRAN.package.GeneNMF |
| Author: | Massimo Andreatta 
[aut, cre],
Santiago Carmona
[aut] |
| Maintainer: | Massimo Andreatta <massimo.andreatta at unige.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.html , GeneNMF.pdf |
| Vignettes: |
Index of GeneNMF vignettes (source) |
Downloads:
| Package source: | GeneNMF_0.9.2.tar.gz |
| Windows binaries: | r-devel: GeneNMF_0.9.2.zip, r-release: GeneNMF_0.9.2.zip, r-oldrel: GeneNMF_0.9.2.zip |
| macOS binaries: | r-release (arm64): GeneNMF_0.9.2.tgz, r-oldrel (arm64): GeneNMF_0.9.2.tgz, r-release (x86_64): GeneNMF_0.9.2.tgz, r-oldrel (x86_64): GeneNMF_0.9.2.tgz |
| Old sources: | GeneNMF archive |
Linking:
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