TcGSA
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:
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 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:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("multtest")The easiest way to get TcGSA is to install it from
CRAN:
install.packages("TcGSA")or to get the development version from GitHub:
#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 package
dearseq which
incorporates similar functionality for analyzing RNA-seq data.
– Boris Hejblum