R Observatory: Metrics for netgsa version 4.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

netgsa

4.0.7Package record

Network-Based Gene Set Analysis

0packages depend

4.4Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Michael HellsternCRAN page ↗GitHub ↗

Carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. Implements methods described in Shojaie A, Michailidis G (2010) doi:10.1093/biomet/asq038, Shojaie A, Michailidis G (2009) doi:10.1089/cmb.2008.0081, and Ma J, Shojaie A, Michailidis G (2016) doi:10.1093/bioinformatics/btw410.

Install

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

install.packages("netgsa", 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("mikehellstern/netgsa")

Development version from mikehellstern/netgsa. 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-netgsa

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

1ERROR12OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64

Packages required but not available: 'graphite', 'RCy3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 6.4 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR11 OK, 1 NOTE, 2 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.0.7

READMEYes · 363 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · does not mention 4.0.7Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 20includes a package overview page
Examples that run: 22%2 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran) · 3 never run
Exported functions with examples: 80%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 65%

Vignettes (1)

Introduction to netgsa HTML

How these are measured

Downloads

4.4K

CRAN downloads in the past year

Rank #9,330 · ~12/day · ~364/mo

Releases R versions

Daily download trend is not available in this view yet.

37230 days

1.1K90 days

4.4K1 year

Compare downloads with other packages →

Also on417 r2u451 bioconda28 c2d4u

How downloads are counted

Repository

mikehellstern/netgsa ↗Account: mikehellsternFork of drjingma/netgsa

4Stars

1Forks

0Open PRs

0Releases

166Commits

4Commit identities

166 commits · Last activity 2021-12-07 · 0% stars, 30d · The default branch showed an older version (4.0.3) than CRAN on 2026-10-22

Responsiveness

not measured

Stars over time

2022-10-26 · 42026-07-07 · 4

How these are measured

PracticesBeta

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

Checks run against github.com/mikehellstern/netgsa on 2026-10-22.

Continuous integration (1)

Travis CI (config file)

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing netgsa adds 41 packages (25 with compiled code, 41 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, igraph 4.8 MB. 5 more not on CRAN are not measured.

Depends (1)

R >= 3.5.0

Imports (19)

AnnotationDbi corpcor data.table dplyr genefilter graph graphite glmnet glassoFast httr igraph magrittrMatrixmsigdbr quadprog RCy3 reshape2 rlang Rcpp

LinkingTo (2)

Rcpp RcppEigen

Suggests (4)

knitrMASSorg.Hs.eg.db rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Michael Hellstern

Author, Maintainer since 4.0.0 (2021) · added in 4.0.0

Jing Ma

Author

Ali Shojaie

Author

Kun Yue

Author · added in 3.1.0

Previously maintained by Jing Ma (1.0 to 3.1.0).

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
4.0.7Latest
record
2026-01-16 · current release · diff ↗
4.0.6
record
2025-07-30 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2023-11-14
4.0.5
record
2023-11-14 · diff ↗
archivedRemoved from CRAN
2023-10-29
email to the maintainer was undeliverable
R
R 4.3.0 released · 2023-04-21
4.0.4
record
2022-10-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
4.0.3
record
2021-12-07 · diff ↗
4.0.2
record
2021-11-17 · diff ↗
4.0.1
record
2021-09-13 · diff ↗
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2021-05-15

Show 13 earlier eventsHide 13 earlier events

4.0.0
record
2021-05-15 · diff ↗ ·
removed 2 exports
prepareAdjacencyMatrix, preparePathways

added 6 exports
NetGSAq, prepareAdjMat, obtainEdgeList, plot.NetGSA, zoomPathway, formatPathways
archivedRemoved from CRAN
2021-04-08
check problems were not corrected in time
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
3.1.0
record
2019-03-27 · diff ↗ ·
removed 1 export
edgelist2adj

added 2 exports
prepareAdjacencyMatrix, preparePathways
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
3.0
record
2016-06-16 · diff ↗ ·
removed 2 exports
covsel, cv.covsel

added 3 exports
netEst.dir, netEst.undir, bic.netEst.undir
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
2.0
record
2015-03-08 · diff ↗
1.0
record
2014-12-02
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-12-02
Total releases: 12 / 12 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 397 KB / 1 file
Download size: 4.5 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("netgsa")

Format

Hellstern, M., Ma, J., Shojaie, A., & Yue, K. (2026). netgsa: Network-Based Gene Set Analysis (Version 4.0.7) [Computer software]. https://doi.org/10.32614/CRAN.package.netgsa

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 netgsa version 4.0.7 [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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