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
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