tcgsaseq
Time-Course Gene Set Analysis for RNA-Seq Data
Analyze RNA-seq data with variance component score test accounting
for data heteroscedasticity through precision weights. Perform both gene-wise and gene set
analyses, and can deal with longitudinal data. Method is detailed in: Agniel & Hejblum
(2017)
tcgsaseq
WARNING: soft-deprecation
tcgsaseq capabilities and features have been incorporated into the
Bioconductor package
dearseq.
tcgsaseq will be kept as the legacy companion package of the 2017
Agniel & Hejblum
Biostatistics
article, but 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.
Overview
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
Installation
The easiest way to get tcgsaseq is to install it from
CRAN:
install.packages("tcgsaseq")
Or to get the development version from GitHub:
#install.packages("devtools")
devtools::install_github("denisagniel/tcgsaseq")
– Denis Agniel and Boris Hejblum