recipe bioconductor-pathvar

Methods to Find Pathways with Significantly Different Variability

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/pathVar.html

License:

LGPL (>= 2.0)

Recipe:

/bioconductor-pathvar/meta.yaml

Links:

biotools: pathvar, doi: 10.7717/peerj.3334

This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability.

package bioconductor-pathvar

(downloads) docker_bioconductor-pathvar

versions:
1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1, 

1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-emt:

depends r-ggplot2:

depends r-gridextra:

depends r-matching:

depends r-mclust:

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-pathvar

and update with::

   mamba update bioconductor-pathvar

To create a new environment, run:

mamba create --name myenvname bioconductor-pathvar

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-pathvar:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda 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-pathvar/README.html)