recipe capcruncher

An end-to-end solution for processing Capture-C, Tri-C and Tiled-C data



Developer docs:


GPL3 / GPL-3.0-or-later



package capcruncher

(downloads) docker_capcruncher



depends click:


depends cooler:

depends duckdb:

depends h5py:

depends loguru:

depends more-itertools:

depends natsort:

depends numpy:

depends pandas:


depends plotly:


depends pyarrow:


depends pybedtools:

depends pyranges:

depends pysam:


depends python:


depends python-xxhash:

depends pyyaml:


depends quarto:

depends ray:

depends seaborn:

depends sh:

depends snakemake:


depends tqdm:

depends trackhub:

depends tracknado:

depends ujson:

depends xopen:



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 capcruncher

and update with::

   mamba update capcruncher

To create a new environment, run:

mamba create --name myenvname capcruncher

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

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