recipe r-sartools

Statistical Analysis of RNA-Seq data

Homepage:

https://github.com/PF2-pasteur-fr/SARTools

License:

GPL-2

Recipe:

/r-sartools/meta.yaml

Links:

biotools: sartools

SARTools provides R tools and an environment for the statistical analysis of RNA-Seq projects load and clean data, produce figures, perform statistical analysis/testing with DESeq2 or edgeR, export results and create final report.

package r-sartools

versions:

1.8.1-2,  1.8.1-1,  1.8.1-0,  1.8.0-0,  1.7.4-0,  1.7.3-3,  1.7.3-2,  1.7.3-1,  1.7.3-0, 

1.8.1-2,  1.8.1-1,  1.8.1-0,  1.8.0-0,  1.7.4-0,  1.7.3-3,  1.7.3-2,  1.7.3-1,  1.7.3-0,  1.7.2-0,  1.7.1-1,  1.7.1-0,  1.6.9-0,  1.6.8-0,  1.6.6-3,  1.6.6-2,  1.6.6-1,  1.6.3-0,  1.6.0-0,  1.5.1-0,  1.4.1-0,  1.3.2-0,  1.2.0-0

depends bioconductor-deseq2:

>=1.32.0

depends bioconductor-edger:

>=3.34.0

depends bioconductor-genefilter:

depends bioconductor-summarizedexperiment:

>=1.6

depends r-ashr:

>=2.2-54

depends r-base:

>=4.3,<4.4.0a0

depends r-bit64:

depends r-blob:

depends r-ggally:

depends r-ggdendro:

depends r-ggplot2:

>=3.3.0

depends r-ggrepel:

depends r-gridextra:

depends r-kableextra:

depends r-knitr:

depends r-optparse:

depends r-rmarkdown:

>=1.4

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 r-sartools

and update with::

   mamba update r-sartools

To create a new environment, run:

mamba create --name myenvname r-sartools

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/r-sartools:<tag>

(see `r-sartools/tags`_ for valid values for ``<tag>``)

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