dearseq

Authors: Boris Hejblum, Denis Agniel, Marine Gauthier, Mélanie Huchon, Iban Larrouture
License: GNU GPL-2

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 (2020). dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, NAR Genomics and Bioinformatics 2(4):lqaa093 DOI: 10.1093/nargab/lqaa093 bioRxiv:635714

♻️ Reproducible code files for the results presented in Gauthier et al. (2020) can be dowloaded here: 👉 🌐 NAR G&B reproducible code files

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

More information about dearseq can be found here: 👉 🌐 pkgdown website

Installation

dearseq is available from Bioconductor

#install.packages("BiocManager")
BiocManager::install("dearseq")

The development version of dearseq is available on GitHub:

#install.packages("BiocManager")
remotes::install_github("borishejblum/dearseq")

– Marine Gauthier, Denis Agniel & Boris Hejblum