recipe bioconductor-mariner

Mariner: Explore the Hi-Cs






Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files, and visualizing the results. Designed for compatibility with plotgardener for visualization.

package bioconductor-mariner

(downloads) docker_bioconductor-mariner



depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-delayedarray:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicranges:


depends bioconductor-hdf5array:


depends bioconductor-interactionset:


depends bioconductor-iranges:


depends bioconductor-plotgardener:


depends bioconductor-plyranges:


depends bioconductor-rhdf5:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends r-abind:

depends r-assertthat:

depends r-base:


depends r-biocmanager:

depends r-colourvalues:

depends r-data.table:

depends r-dbscan:

depends r-glue:

depends r-magrittr:

depends r-progress:

depends r-purrr:

depends r-rcolorbrewer:

depends r-rlang:

depends r-strawr:




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-mariner

and update with::

   mamba update bioconductor-mariner

To create a new environment, run:

mamba create --name myenvname bioconductor-mariner

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

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