recipe cooler

Sparse binary format for genomic interaction matrices



BSD / BSD-3-Clause




doi: 0.1093/bioinformatics/btz540

package cooler

(downloads) docker_cooler



depends asciitree:

depends click:


depends cytoolz:

depends dask:

depends h5py:


depends hdf5:

depends multiprocess:

depends numpy:


depends pairix:

depends pandas:


depends pyfaidx:

depends pysam:


depends python:


depends pyyaml:

depends scipy:

depends simplejson:



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 cooler

and update with::

   mamba update cooler

To create a new environment, run:

mamba create --name myenvname cooler

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

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