GitHub - sistm/TcGSA: R package for Time-course Gene Set Analysis (original) (raw)

TcGSA

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Overview

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

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

Hejblum, BP, Skinner, J, & Thiébaut, R (2015). Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. PLOS Computational Biology, 11(6):e1004310. <doi: 10.1371/journal.pcbi.1004310>

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("multtest")

The easiest way to get TcGSA is to install it fromCRAN:

install.packages("TcGSA")

or to get the development version fromGitHub:

#install.packages("devtools") devtools::install_github("sistm/TcGSA")

Microarrays vs RNA-seq

TcGSA relies on a Gaussian assumption for the expression data, which is suitable for normalized microarray data. Due to their count and heteroskedastic nature, RNA-seq data need to be handled differently and_TcGSA cannot deal with RNA-seq data_. For RNA-seq data, please have a look at the Bioconductor packagedearseq which incorporates similar functionality for analyzing RNA-seq data.

– Boris Hejblum