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