README.md

In dearseq: Differential Expression Analysis for RNA-seq data through a robust variance component test

dearseq

Overview

dearseq is a package for analyzing RNA-seq data. The 2 main functions of the package are dear_seq() and dgsa_seq():

• Gene-wise Differential Analysis of RNA-seq data can be performed using the function dear_seq().
• Gene Set Analysis of RNA-seq data can be performed using the function dgsa_seq().

The methods implemented in this package are detailed in the following articles:

Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2019). dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, bioRxiv 635714. DOI: 10.1101/635714

Agniel D & Hejblum BP (2017). Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics, 18(4):589-604. arXiv:1605.02351 DOI: 10.1093/biostatistics/kxx005

Installation

dearseq is currently under review to be included in Bioconductor

Meanwhile, the easiest way to get dearseq is to install its development version from the dev branch on GitHub:

#install.packages("devtools")
devtools::install_github("borishejblum/dearseq", ref="dev")

– Marine Gauthier, Denis Agniel & Boris Hejblum

dearseq documentation built on Nov. 8, 2020, 5:49 p.m.