R Observatory: Metrics for TcGSA version 0.12.13

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TcGSA

0.12.13Package record

Time-Course Gene Set Analysis

0packages depend

3.8Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Boris P HejblumCRAN page ↗GitHub ↗Website ↗Issues ↗

Implementation of Time-course Gene Set Analysis (TcGSA), a method for analyzing longitudinal gene-expression data at the gene set level. Method is detailed in: Hejblum, Skinner & Thiebaut (2015) <doi: 10.1371/journal.pcbi.1004310>.

Changes in 0.12.13

improved documentation with correct links for CRAN static html and update URLs

From NEWS.md in the release

Install

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

install.packages("TcGSA", 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("sistm/TcGSA")

Development version from sistm/TcGSA. 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-tcgsa

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Boris P Hejblum <boris.hejblum@u-bordeaux.fr>’

Found the following (possibly) invalid URLs:
  URL: https://docs.gsea-msigdb.org/#GSEA/Data_Formats/#gmt-gene-matrix-transposed-file-format-gmt/
    From: inst/doc/TcGSA_userguide.html
    Message: Invalid URL: '#' not allowed in fragment

CRAN check page ↗

Slowest check: 5.3 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE11 OK, 2 NOTE2026-05-30
WARNING10 OK, 2 NOTE, 1 WARNING2026-05-28
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.12.13

READMEYes · 203 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.12.13Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 18 (2 internal)includes a package overview page
Examples that run: 100%15 run in a plain check (13 of them under a condition)
Exported functions with examples: 92%
Documented parameters: 96%
Return-value docs: 92%
Help pages citing references: 67%

Vignettes (1)

TcGSA_userguide

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #11,605 · ~10/day · ~313/mo

Releases R versions

Daily download trend is not available in this view yet.

42830 days

93290 days

3.8K1 year

Compare downloads with other packages →

Also on92 r2u58 c2d4u

How downloads are counted

Repository

sistm/tcgsa ↗Organization: sistm

6Stars

2Forks

2Open issues

0Open PRs

3Releases

257Commits

8Commit identities

License file reads as GPL-2.0 · 257 commits · Last activity 2025-07-26

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-01-01 · 62026-07-07 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/sistm/tcgsa on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-07-22 · The repository has a site deploy workflow

pkgdown site last built 2025-07-22

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing TcGSA adds 33 packages (18 with compiled code, 39 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, lme4 4.1 MB. 1 more not on CRAN is not measured.

Depends (2)

R >= 3.0.2ggplot2

Imports (13)

lme4 reshape2 GSA multtestclustercowplotgraphicsgrDevicesgtools stringrsplinesstatsutils

LinkingTo (0)

none

Suggests (8)

BiocManager foreachparalleldoParallel dearseq knitr GEOquery 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 (3)

Boris P Hejblum

Author, Maintainer since 0.9.8 (2014)

Damien Chimits

Author · added in 0.10.1

Anthony Devaux

Author · added in 0.11.1

Listed in earlier versions (2)

Boris P. Hejblum

no longer listed · 0.9.8 to 0.12.4

Boris P

no longer listed · 0.12.7 to 0.12.13

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.12.13Latest
record
2025-07-22 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
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
0.12.10
record
2022-02-28 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.12.7
record
2020-01-23 · diff ↗
0.12.4
record
2019-04-30 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.12.2
record
2019-01-16 · diff ↗
0.11.1
record
2018-06-08 · diff ↗ ·
removed 1 export
rmixchisq

added 5 exports
dchisqmix, pchisqmix, plotMultipleGS, qchisqmix, rchisqmix
R
R 3.5.0 released · 2018-04-23
0.10.5
record
2017-05-03 · diff ↗

Show 6 earlier eventsHide 6 earlier events

R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.10.1
record
2015-12-22 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 11 exports
TcGSA.LR, TcGSA.LR.parallel, clustTrend, multtest.TcGSA, plot1GS, plotFit.GS, plotPat.1GS, plotPat.TcGSA, plotSelect.GS, rmixchisq, signifLRT.TcGSA
R
R 3.2.0 released · 2015-04-16
0.9.8
record
2014-04-28
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-04-28
Total releases: 9 / 12 yrs
License: GPL-2 | file LICENSE OSI · relicensed from LGPL-3 | file LICENSE in 0.10.1
Minimum R: ≥ 3.0.2
Bundled data: 169 KB / 1 file
Download size: 364 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("TcGSA")

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

It points to 10.1371/journal.pcbi.1004310.

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 TcGSA version 0.12.13 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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