recipe hicstuff

General purpose stuff to generate and handle Hi-C data in its simplest form.




GPL3 / GPL-3.0-only



package hicstuff

(downloads) docker_hicstuff



depends biopython:

depends bowtie2:

depends cooler:

depends coreutils:

depends docopt:

depends matplotlib-base:

depends minimap2:

depends numpy:

depends pandas:

depends pyfastx:

depends pysam:

depends python:


depends requests:

depends samtools:

depends scikit-learn:

depends scipy:



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 hicstuff

and update with::

   mamba update hicstuff

To create a new environment, run:

mamba create --name myenvname hicstuff

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

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