TcGSA

0.12.13

Time-Course Gene Set Analysis

0packages depend

3.7Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Boris P HejblumFirst published 2014-04-289 releasesCRAN page ↗GitHub ↗

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>.

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.

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 4.4 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-05-30
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-28
10 OK · 2 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 203 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 92%
References docs: 67%

Downloads

3.7K

CRAN downloads in the past year

Rank #11,367 · ~10/day · ~312/mo

Releases R versions

Daily download trend is not available in this view yet.

23130 days

89590 days

3.7K1 year

Compare downloads with other packages →

Also on119 r2u27 c2d4u

Repository

GitHub ↗ sistm/tcgsa

6Stars

2Forks

2Open issues

0Open PRs

3Releases

257Commits

8Contributors

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

Stars over time

2025-01-01 · 62026-07-07 · 6

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/sistm/tcgsa on 2026-07-31.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Boris P Hejblum

Author, Maintainer

Authors (3)

Boris P Hejblum

Author, Maintainer

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

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.12.13Latest
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
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
2020-01-23 · diff ↗
0.12.4
2019-04-30 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.12.2
2019-01-16 · diff ↗
0.11.1
2018-06-08 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.10.5
2017-05-03 · diff ↗

Show 6 earlier events

R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.10.1
2015-12-22 · diff ↗
R
R 3.2.0 released · 2015-04-16
0.9.8
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
Minimum R: ≥ 3.0.2
Bundled data: 169 KB / 1 file
Download size: 364 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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