R Observatory: Metrics for liger version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-06-14. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 2.0.1, its last release before removal.

liger

2.0.1Package record

Lightweight Iterative Geneset Enrichment

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Jean FanCRAN page ↗GitHub ↗

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. The original algorithm is detailed in Subramanian et al. with 'Java' implementations available through the Broad Institute (Subramanian et al. 2005 doi:10.1073/pnas.0506580102). The 'liger' package provides a lightweight R implementation of this enrichment test on a list of values (Fan et al., 2017 doi:10.5281/zenodo.887386). Given a list of values, such as p-values or log-fold changes derived from differential expression analysis or other analyses comparing biological states, this package enables you to test a priori defined set of genes for enrichment to enable interpretability of highly significant or high fold-change genes.

Install

R (source archive)pak (dev)

url <- "https://cran.r-project.org/src/contrib/Archive/liger/liger_2.0.1.tar.gz"
pkgFile <- "liger_2.0.1.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (2.0.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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

Development version from JEFworks/liger. Installs pak first if it is not already available.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

READMEYes · 215 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · does not mention 2.0.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 5includes a package overview page
Examples that run: 100%3 run in a plain check
Exported functions with examples: 100%
Documented parameters: 94%
Return-value docs: 0%
Help pages citing references: 0%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on357 r2u7 autocran7K bioconda89 c2d4u

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (5)

graphicsstatsRcpp matrixStatsparallel

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Jean Fan

Author, Maintainer since 0.1 (2018)

Peter Kharchenko

Author

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-06-14
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
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
2.0.1
record
2021-01-25 · diff ↗
1.1.2
record
2020-07-16 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0
record
2019-01-03 · diff ↗
0.1
record
2018-06-14
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-06-14
Total releases: 4 / 8 yrs
License: GPL-3 | file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 1.8 MB / 2 files

Cite

Cite this package

Run in R for the authors' entry:

citation("liger")

The package provides a citation file, so citation() returns the authors' own entry.

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 liger version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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