Time-Course Gene Set Analysis

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) .

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TcGSA is a package which performs Time-course Gene Set Analysis from microarray data, and provide nice representations of its results.

On top of the CRAN help pdf-file, the following article explains what TcGSA is about:


TcGSA imports the multtest package which is not available on CRAN, but is available on the Bioconductor repository. Before installing TcGSA, be sure to have this multtest package installed. If not, you can do so by running the following:


The easiest way to get TcGSA is to install it from CRAN:


or to get the development version from GitHub:


-- Boris Hejblum


News about the TcGSA R package

Main changes in Version 0.12.4 (2019-04-30) --- this is only a minor release:

  • Prevent the simultaneous use of baseline and group.var in plotting functions
  • Added na.rmsupport for aggreg.fun everywhere

Main changes in Version 0.11.0 (2018-06-07) --- this is only a minor release:

  • Added a vignette
  • p-values are no-longer simulated but computed from asymptotic chi^2 mixture

Main changes in Version 0.10.7 (2017-12-05) --- this is only a minor release:

  • Added plotMultipleGS function

Main changes in Version 0.10.6 (2017-10-12) --- this is only a minor release:

  • Added a NEWS.md file to track changes to the package.

Main changes in Version 0.10.5 (2017-05-03) --- this is only a minor release:

  • Bug fix: plot.TcGSA better handles more various geneses names

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.


0.12.7 by Boris P Hejblum, 2 years ago

Report a bug at https://github.com/borishejblum/TcGSA/issues

Browse source code at https://github.com/cran/TcGSA

Authors: Boris P Hejblum [aut, cre] , Damien Chimits [aut] , Anthony Devaux [aut]

Documentation:   PDF Manual  

GPL-2 | file LICENSE license

Imports lme4, reshape2, GSA, multtest, cluster, cowplot, graphics, grDevices, gtools, stringr, splines, stats, utils

Depends on ggplot2

Suggests BiocManager, foreach, parallel, doParallel, tcgsaseq, knitr, GEOquery, rmarkdown

See at CRAN