recipe icount

Computational pipeline for analysis of iCLIP data






iCount is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions.

package icount

(downloads) docker_icount



depends bedtools:


depends cutadapt:


depends matplotlib:

depends numpy:

depends numpydoc:

depends pandas:

depends pybedtools:

depends pysam:

depends python:


depends sphinx:


depends star:



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 icount

and update with::

   mamba update icount

To create a new environment, run:

mamba create --name myenvname icount

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

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