recipe bioconductor-cntools

Convert segment data into a region by sample matrix to allow for other high level computational analyses.

Homepage:

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

License:

LGPL-3.0-only

Recipe:

/bioconductor-cntools/meta.yaml

Links:

biotools: cntools, doi: 10.1038/nmeth.3252

This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data

package bioconductor-cntools

(downloads) docker_bioconductor-cntools

versions:
1.58.0-1,  1.58.0-0,  1.56.0-0,  1.54.0-1,  1.54.0-0,  1.50.0-2,  1.50.0-1,  1.50.0-0,  1.48.0-0, 

1.58.0-1,  1.58.0-0,  1.56.0-0,  1.54.0-1,  1.54.0-0,  1.50.0-2,  1.50.0-1,  1.50.0-0,  1.48.0-0,  1.46.0-1,  1.46.0-0,  1.44.0-0,  1.42.0-0,  1.40.0-1,  1.38.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

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-cntools

and update with::

   mamba update bioconductor-cntools

To create a new environment, run:

mamba create --name myenvname bioconductor-cntools

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-cntools:<tag>

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