GeneNMF

0.9.2

Non-Negative Matrix Factorization for Single-Cell Omics

0packages depend

7.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Massimo AndreattaFirst published 2024-02-295 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)openSUSE (OBS)

install.packages("GeneNMF", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("carmonalab/GeneNMF")

Development version from carmonalab/GeneNMF. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-genenmf

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-GeneNMF

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 7.7 min · r-devel-linux-x86_64-fedora-clang

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

7.7K

CRAN downloads in the past year

Rank #4,727 · ~21/day · ~645/mo

GeneNMF Releases R versions

Daily download trend is not available in this view yet.

46230 days

1.9K90 days

7.7K1 year

Compare downloads with other packages →

Also on99 r2u9 autocran

Repository

GitHub ↗ carmonalab/genenmf

197Stars

11Forks

6Open issues

0Open PRs

5Releases

130Commits

4Contributors

130 commits · Last activity 2026-07-21 · +2.6% stars, 30d

Repository practices

Upstream repositoryBeta

Checks run against github.com/carmonalab/genenmf on 2026-07-19.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3.0

Imports (13)

RcppMLMatrixstatsmethodsutilsSeuratclusterlsa irlba pheatmap dendextend viridis colorspace

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown fgsea msigdbr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Massimo Andreatta

Author, Maintainer

Authors (2)

Massimo Andreatta

Author, Maintainer

Santiago Carmona

Author

Package Timeline

5 releases. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.9.2Latest
2025-09-11 · current release · diff ↗
0.8.0
2025-04-24 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.6.2
2024-11-12 · diff ↗
0.6.0
2024-07-22 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.4.0
2024-02-29
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-02-29
Total releases: 5 / 2 yrs
License: GPL-3 OSI
Download size: 556 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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