R Observatory: Metrics for LEANR version 1.4.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-04-20. Its history is shown below.

Reason: issues were not corrected despite reminders

Details below reflect version 1.4.9, its last release before removal.

LEANR

1.4.9

Finds "Local Subnetworks" Within an Interaction Network which Show Enrichment for Differentially Expressed Genes

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Frederik Gwinner1 releasesCRAN page ↗

Implements the method described in "Network-based analysis of omics data: The LEAN method" [Gwinner Boulday (2016) DOI:10.1093/bioinformatics/btw676] Given a protein interaction network and a list of p-values describing a measure of interest (as e.g. differential gene expression) this method computes an enrichment p-value for the protein neighborhood of each gene and compares it to a background distribution of randomly drawn p-values. The resulting scores are corrected for multiple testing and significant hits are returned in tabular format.

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/LEANR/LEANR_1.4.9.tar.gz"
pkgFile <- "LEANR_1.4.9.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 (1.4.9) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-leanr

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-LEANR

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.18

not tracked

Coverage

0%

Documentation · exports

2

Dependencies · direct

Documentation

READMEYes · 142 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 27%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on107 r2u17 autocran

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (3)

R >= 2.14igraph foreach

Imports (0)

none

LinkingTo (0)

none

Suggests (5)

knitr doMC rmarkdown ROCR testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Other (1)

Frederik Gwinner

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-04-20
issues were not corrected despite reminders
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
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.4.9
2016-11-12
R
R 3.3.0 released · 2016-05-03

Package metadata

Total releases: 1
License: GPL-3 OSI
Minimum R: ≥ 2.14
Bundled data: 1.4 MB / 7 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("LEANR")

Format

Gwinner, F. (n.d.). LEANR: Finds "Local Subnetworks" Within an Interaction Network which Show Enrichment for Differentially Expressed Genes (Version 1.4.9) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=LEANR

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 LEANR version 1.4.9 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →