recipe bioconductor-zenith

Gene set analysis following differential expression using linear (mixed) modeling with dream

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-zenith/meta.yaml

Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method from the limma package proposed by Wu and Smyth (2012). Zenith is a simple extension of camera to be compatible with linear mixed models implemented in variancePartition::dream().

package bioconductor-zenith

versions:

1.4.2-0,  1.2.0-0,  1.0.0-0

depends bioconductor-enrichmentbrowser:

>=2.32.0,<2.33.0

depends bioconductor-gseabase:

>=1.64.0,<1.65.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-variancepartition:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-msigdbr:

>=7.5.1

depends r-progress:

depends r-rdpack:

depends r-reshape2:

depends r-rfast:

depends r-tidyr:

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-zenith

and update with::

   mamba update bioconductor-zenith

To create a new environment, run:

mamba create --name myenvname bioconductor-zenith

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-zenith:<tag>

(see `bioconductor-zenith/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-zenith/README.html)