recipe bioconductor-bader

Bayesian Analysis of Differential Expression in RNA Sequencing Data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/BADER.html

License:

GPL-2

Recipe:

/bioconductor-bader/meta.yaml

Links:

biotools: bader, doi: 10.1038/nmeth.3252

For RNA sequencing count data, BADER fits a Bayesian hierarchical model. The algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.

package bioconductor-bader

versions:

1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-2,  1.36.0-1,  1.36.0-0,  1.32.0-2,  1.32.0-1,  1.32.0-0, 

1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-2,  1.36.0-1,  1.36.0-0,  1.32.0-2,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.1-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

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-bader

and update with::

   mamba update bioconductor-bader

To create a new environment, run:

mamba create --name myenvname bioconductor-bader

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-bader:<tag>

(see `bioconductor-bader/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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