dearseq-package {dearseq}R Documentation

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

Description

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Differential Expression Analysis 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 repeated or longitudinal data. Methods are detailed in: i) 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 ; and ii) Gauthier M, Agniel D, ThiƩbaut 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.

Details

Analysis of RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights. Performs gene-wise analysis as well as gene set analysis, including for complex experimental designs such as longitudinal data.

Package: dearseq
Type: Package
Version: 1.5.1
Date: 2021-09-01
License: GPL-2

The two main functions of the dearseq package are dear_seq and dgsa_seq.

Author(s)

Maintainer: Boris P. Hejblum boris.hejblum@u-bordeaux.fr

Authors:

References

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. DOI: 10.1093/biostatistics/kxx005. arXiv:1605.02351.

Gauthier M, Agniel D, ThiƩbaut 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. DOI: 10.1101/635714

See Also

Useful links:


[Package dearseq version 1.6.0 Index]