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.


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Overview

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:

Installation

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:

source("http://bioconductor.org/biocLite.R")
biocLite("multtest")

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

install.packages("TcGSA")

or to get the development version from GitHub:

devtools::install_github("borishejblum/TcGSA")

-- Boris Hejblum

News

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.

install.packages("TcGSA")

0.12.4 by Boris P. Hejblum, 7 months 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, gplots, graphics, grDevices, gtools, stringr, splines, stats, utils

Depends on ggplot2

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


See at CRAN