tcgsaseq capabilities and features have been incorporated into the
Bioconductor package
dearseq.
tcgsaseq is the legacy companion package of the 2017 Agniel & Hejblum
Biostatistics
article. It has been archived on CRAN and will not be further developped
or extended.
If you are interested in using tcgsaseq, you should probably rather look
into the newer and more comprehensive dearseq package.
tcgsaseq is a package for analyzing RNA-seq data. The 2 main functions
of the package are varcompseq and tcgsa_seq:
- Gene-wise Differential Analysis of RNA-seq data can be performed
using the function
varcompseq. - Gene Set Analysis of RNA-seq data can be performed using the
function
tcgsa_seq.
The method implemented in this package is detailed in the following article:
Agniel D & Hejblum BP (2017). Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, 2017, Biostatistics, 18(4):589-604. arXiv:1605.02351 DOI: 10.1093/biostatistics/kxx005
The easiest way to get tcgsaseq is to install it from
GitHub:
#install.packages("devtools")
devtools::install_github("denisagniel/tcgsaseq")– Denis Agniel and Boris Hejblum