recipe bioconductor-regionereloaded

RegioneReloaded: Multiple Association for Genomic Region Sets

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-regionereloaded/meta.yaml

RegioneReloaded is a package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and the creation of ready-to-publish graphs. It takes over and expands on all the features of its predecessor regioneR. It also incorporates a strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. RegioneReloaded builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.

package bioconductor-regionereloaded

(downloads) docker_bioconductor-regionereloaded

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-regioner:

>=1.34.0,<1.35.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

depends r-ggplot2:

depends r-ggrepel:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rtsne:

depends r-scales:

depends r-umap:

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-regionereloaded

and update with::

   mamba update bioconductor-regionereloaded

To create a new environment, run:

mamba create --name myenvname bioconductor-regionereloaded

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-regionereloaded:<tag>

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

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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-regionereloaded/README.html)