R Observatory: Metrics for GeneNMF version 0.9.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GeneNMF

0.9.2

Non-Negative Matrix Factorization for Single-Cell Omics

0packages depend

7.8Kdownloads / 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)Fedora (COPR)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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-GeneNMF

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# 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: 5.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

13

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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

Show 2 earlier snapshots

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

READMEYes · 552 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 90%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

7.8K

CRAN downloads in the past year

Rank #4,600 · ~21/day · ~651/mo

Releases R versions

Daily download trend is not available in this view yet.

40030 days

1.7K90 days

7.8K1 year

Compare downloads with other packages →

Also on105 r2u

Repository

GitHub ↗ carmonalab/genenmf

206Stars

10Forks

6Open issues

0Open PRs

5Releases

135Commits

5Contributors

135 commits · Last activity 2026-07-21 · +5.1% stars, 30d

Stars over time

2025-07-31 · 1402026-08-13 · 206

Repository practices

Upstream repositoryBeta

Checks run against github.com/carmonalab/genenmf on 2026-08-16.

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. Pick two to compare their code metrics. 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
Minimum R: ≥ 4.3.0
Bundled data: 486 KB / 1 file
Download size: 556 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GeneNMF")

Format

Andreatta, M., & Carmona, S. (2025). GeneNMF: Non-Negative Matrix Factorization for Single-Cell Omics (Version 0.9.2) [Computer software]. https://doi.org/10.32614/CRAN.package.GeneNMF

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for GeneNMF version 0.9.2 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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