- recipe bioconductor-dearseq
Differential Expression Analysis for RNA-seq data through a robust variance component test
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/dearseq.html
- License:
GPL-2 | file LICENSE
- Recipe:
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:
1.14.0-0
,1.12.1-0
,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:
>=4.3,<4.4.0a0
- depends r-compquadform:
- depends r-dplyr:
- depends r-ggplot2:
- depends r-kernsmooth:
- depends r-magrittr:
- depends r-matrixstats:
- depends r-patchwork:
- depends r-pbapply:
- depends r-reshape2:
- depends r-rlang:
- depends r-scattermore:
- depends r-statmod:
- depends r-survey:
- depends r-tibble:
- depends r-viridislite:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-dearseq and update with:: mamba update bioconductor-dearseq
To create a new environment, run:
mamba create --name myenvname bioconductor-dearseq
with
myenvname
being a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-dearseq:<tag> (see `bioconductor-dearseq/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-dearseq/README.html)