recipe cytocad

Large copy-number variation detector with low-depth whole-genome sequencing data



GPL3 / GPL-3.0-or-later



package cytocad

(downloads) docker_cytocad



depends bedtools:


depends libgcc-ng:


depends librsvg:


depends matplotlib-base:


depends numpy:


depends pybedtools:


depends pysam:


depends python:


depends python_abi:

3.10.* *_cp310

depends ruptures:


depends samtools:


depends scipy:


depends tagore:




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 cytocad

and update with::

   mamba update cytocad

To create a new environment, run:

mamba create --name myenvname cytocad

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 `cytocad/tags`_ for valid values for ``<tag>``)

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