dearseq-package {dearseq} | R Documentation |
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.
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
.
Maintainer: Boris P. Hejblum boris.hejblum@u-bordeaux.fr
Authors:
Denis Agniel denis.agniel@gmail.com
Marine Gauthier marine.gauthier@u-bordeaux.fr
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
Useful links:
Report bugs at https://github.com/borishejblum/dearseq/issues