recipe bioconductor-hicool







HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.

package bioconductor-hicool

(downloads) docker_bioconductor-hicool



depends bioconductor-basilisk:


depends bioconductor-biocio:


depends bioconductor-genomicranges:


depends bioconductor-hicexperiment:


depends bioconductor-interactionset:


depends bioconductor-iranges:


depends bioconductor-s4vectors:


depends r-base:


depends r-dplyr:

depends r-plotly:

depends r-reticulate:

depends r-rmarkdown:

depends r-rmdformats:

depends r-sessioninfo:

depends r-stringr:

depends r-vroom:



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 bioconductor-hicool

and update with::

   mamba update bioconductor-hicool

To create a new environment, run:

mamba create --name myenvname bioconductor-hicool

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 `bioconductor-hicool/tags`_ for valid values for ``<tag>``)

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