recipe bioconductor-cntools

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







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



depends bioconductor-genefilter:


depends bioconductor-genefilter:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends r-base:




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<tag>

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

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