recipe bioconductor-dearseq

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

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/dearseq.html

License:

GPL-2 | file LICENSE

Recipe:

/bioconductor-dearseq/meta.yaml

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, 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.

package bioconductor-dearseq

Versions:

1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

Depends:

• r-base >=4.2,<4.3.0a0

• r-compquadform

• r-dplyr

• r-ggplot2

• r-kernsmooth

• r-magrittr

• r-matrixstats

• r-patchwork

• r-pbapply

• r-reshape2

• r-rlang

• r-scattermore

• r-statmod

• r-survey

• r-tibble

• r-viridislite

Required By:

• bioconductor-benchdamic

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-dearseq

and update with:

conda update bioconductor-dearseq

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-dearseq:<tag>

(see bioconductor-dearseq/tags for valid values for <tag>)

Download stats

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