recipe bioconductor-concordexr

Calculate the concordex coefficient

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-concordexr/meta.yaml

Many analysis workflows include approximation of a nearest neighbors graph followed by clustering of the graph structure. The concordex coefficient estimates the concordance between the graph and clustering results. The package 'concordexR' is an R implementation of the original concordex Python-based command line tool.

package bioconductor-concordexr

(downloads) docker_bioconductor-concordexr

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cli:

depends r-ggplot2:

depends r-matrix:

depends r-pheatmap:

depends r-rlang:

depends r-scales:

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-concordexr

and update with::

   mamba update bioconductor-concordexr

To create a new environment, run:

mamba create --name myenvname bioconductor-concordexr

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-concordexr:<tag>

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