R Observatory: Metrics for rliger version 2.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rliger

2.2.1

Linked Inference of Genomic Experimental Relationships

1packages depend

125.3Kdownloads / year

69.4%test coverage

10/13checks pass

Overview

About

Maintained by Yichen WangFirst published 2021-01-258 releasesCRAN page ↗GitHub ↗

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) doi:10.1016/j.cell.2019.05.006, and Liu J, Gao C, Sodicoff J, et al (2020) doi:10.1038/s41596-020-0391-8 for more details.

Install

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

install.packages("rliger", 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("welch-lab/liger")

Development version from welch-lab/liger. 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-rliger

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

Health

CRAN checks

3ERROR10OK

Failing flavors

ERROR r-devel-linux-x86_64-debian-clang
ERROR r-devel-linux-x86_64-debian-gcc
ERROR r-release-linux-x86_64

Slowest check: 17.9 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.08

69.4%

Coverage · measured lines

99%

Documentation · exports

21

Dependencies · direct

Check history

ERROR2026-08-13
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 9 earlier snapshots

ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-16
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-13
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 680 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 82%
Return-value docs: 87%
References docs: 9%

Downloads

125.3K

CRAN downloads in the past year

Rank #3,240 · ~343/day · ~10.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

91430 days

3.5K90 days

125.3K1 year

Compare downloads with other packages →

Also on551 r2u

Repository

GitHub ↗ welch-lab/liger

432Stars

80Forks

36Open issues

11Open PRs

14Releases

949Commits

17Contributors

rsingle-cellnonnegative-matrix-factorization

License GPL-3.0 · 949 commits · Last activity 2026-02-04 · +0.2% stars, 30d

Stars over time

2025-08-04 · 4132026-07-27 · 432

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/welch-lab/liger on 2026-08-16.

Continuous integration (1)

GitHub Actions

Coverage (2)

Codecov.covrignore

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

Dependencies

Declared dependencies

45 external dependencies (excludes base and recommended)

Depends (4)

R >= 3.5methodsstatsutils

Imports (18)

cli DelayedArray dplyr ggplot2gridHDF5Array hdf5r leidenAlg lifecycle magrittrMatrixRANN Rcpp RcppPlanc rlang S4Vectors scales uwot

LinkingTo (3)

Rcpp RcppArmadillo RcppProgress

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

scCustomize

Code & Tests

Datasets

People & History

People (11)

Maintainer (1)

Yichen Wang

Author, Maintainer · added in 1.0.1

Authors (7)

Yichen Wang

Author, Maintainer · added in 1.0.1

Author

Author, Contributor

Author

Author, Contributor

Author, Contributor

Author

Contributors (7)

Author, Contributor

Author, Contributor

Author, Contributor

Contributor

Contributor

Contributor

Contributor · added in 2.0.0

Package Timeline

8 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
2.2.1Latest
2025-08-26 · current release · diff ↗
2.2.0
2025-05-02 · diff ↗
unarchivedReturned to CRAN
2025-05-02
archivedRemoved from CRAN
2025-04-19
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
2.1.0
2024-10-30 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.0.1
2024-04-05 · diff ↗
2.0.0
2024-03-20 · diff ↗
1.0.1
2023-11-09 · diff ↗
unarchivedReturned to CRAN
2023-11-09
archivedRemoved from CRAN
2023-10-27
requires archived package 'riverplot'
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18

Show 3 earlier events

1.0.0
2021-04-20 · diff ↗
0.5.0
2021-01-25
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-25
Total releases: 8 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 392 KB / 6 files
Download size: 1.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rliger")

Format

Wang, Y., Gao, C., Hoffman, P., Korsunsky, I., Kozareva, V., Lee, R., Liu, J., Macosko, E., Robbins, A., Sodicoff, J., & Welch, J. (2025). rliger: Linked Inference of Genomic Experimental Relationships (Version 2.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.rliger

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 rliger version 2.2.1 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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