Package: GeneNMF
Type: Package
Title: Non-Negative Matrix Factorization for Single-Cell Omics
Version: 0.9.5
Authors@R: c(
  person('Massimo', 'Andreatta',
    email = 'massimo.andreatta@unige.ch',
    role = c('aut','cre'),
    comment = c(ORCID = '0000-0002-8036-2647')),
  person('Santiago', 'Carmona',
    email = 'santiago.carmona@unige.ch',
    role = c('aut'),
    comment = c(ORCID = '0000-0002-2495-0671')) 
  )
Description: 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.
biocViews:
Depends: R (>= 4.3.0)
Imports: RcppML, Matrix, stats, methods, utils, Seurat (>= 4.3.0),
        cluster, lsa, pheatmap, dendextend, viridis, colorspace
Suggests: knitr, rmarkdown, fgsea, msigdbr
VignetteBuilder: knitr
URL: https://github.com/carmonalab/GeneNMF
BugReports: https://github.com/carmonalab/GeneNMF/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://carmonalab.r-universe.dev
Date/Publication: 2026-06-05 13:52:46 UTC
RemoteUrl: https://github.com/carmonalab/GeneNMF
RemoteRef: HEAD
RemoteSha: 355c4664732ab9a5a62f1b7c38faca8bf3c4c689
NeedsCompilation: no
Packaged: 2026-06-05 14:53:55 UTC; root
Author: Massimo Andreatta [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-8036-2647>),
  Santiago Carmona [aut] (ORCID: <https://orcid.org/0000-0002-2495-0671>)
Maintainer: Massimo Andreatta <massimo.andreatta@unige.ch>