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:

/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:

1.14.0-0,  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:

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>``)

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