:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'hicexplorer' .. highlight: bash hicexplorer =========== .. conda:recipe:: hicexplorer :replaces_section_title: :noindex: Set of programs to process\, analyze and visualize Hi\-C and capture Hi\-C data :homepage: https://github.com/deeptools/HiCExplorer :license: GPL3 :recipe: /`hicexplorer `_/`meta.yaml `_ :links: doi: :doi:`10.1093/nar/gky504`, doi: :doi:`10.1093/nar/gkaa220`, doi: :doi:`10.1093/gigascience/giac061`, usegalaxy-eu: :usegalaxy-eu:`hicexplorer_hicplotviewpoint` .. conda:package:: hicexplorer |downloads_hicexplorer| |docker_hicexplorer| :versions: .. raw:: html
3.7.3-03.7.2-13.7.2-03.7.1-03.7-03.6-03.5.3-03.5.2-03.5.1-0 ``3.7.3-0``,  ``3.7.2-1``,  ``3.7.2-0``,  ``3.7.1-0``,  ``3.7-0``,  ``3.6-0``,  ``3.5.3-0``,  ``3.5.2-0``,  ``3.5.1-0``,  ``3.5-0``,  ``3.4.3-1``,  ``3.4.3-0``,  ``3.4.2-0``,  ``3.4.1-1``,  ``3.4.1-0``,  ``3.4-0``,  ``3.3.1-0``,  ``3.3-0``,  ``3.2-0``,  ``3.1-0``,  ``3.0.2-0``,  ``3.0.1-0``,  ``2.2.3-0``,  ``2.2.2-0``,  ``2.2.1-0``,  ``2.2-1``,  ``2.2-0``,  ``2.2beta-0``,  ``2.1.4-3``,  ``2.1.4-2``,  ``2.1.3-0``,  ``2.1.2-0``,  ``2.1.1-1``,  ``2.1.1-0``,  ``2.1-0``,  ``2.1alpha1-0``,  ``2.0-1``,  ``2.0-0``,  ``1.8.1-0``,  ``1.8-2``,  ``1.8-1``,  ``1.8-0``,  ``1.7.2-0``,  ``1.7.1-0``,  ``1.6.1-0``,  ``1.6-0``,  ``1.4-0``,  ``1.3-0``,  ``1.2-0``,  ``1.1a-0``,  ``0.1-0`` .. raw:: html
:depends biopython: :depends cleanlab: ``>=2.5`` :depends cooler: ``>=0.9.3`` :depends fit_nbinom: ``>=1.2`` :depends future: :depends hic2cool: ``>=0.8.3`` :depends hicmatrix: ``>=17`` :depends hyperopt: ``>=0.2.7`` :depends imbalanced-learn: ``>=0.11`` :depends intervaltree: :depends ipykernel: ``>=6.25.2`` :depends jinja2: :depends krbalancing: ``>=0.0.5`` :depends matplotlib-base: ``>=3.6`` :depends numpy: ``>=1.19`` :depends pandas: ``>=2.0`` :depends psutil: :depends pybedtools: ``>=0.9`` :depends pybigwig: :depends pygenometracks: ``>=3.8`` :depends pysam: :depends pytables: :depends python: ``>=3.8`` :depends python-graphviz: ``>=0.20`` :depends scikit-learn: ``>=1.3.1`` :depends scipy: ``>=1.10`` :depends tqdm: ``>=4.66`` :depends unidecode: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 hicexplorer and update with:: mamba update hicexplorer To create a new environment, run:: mamba create --name myenvname hicexplorer 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 quay.io/biocontainers/hicexplorer: (see `hicexplorer/tags`_ for valid values for ````) .. |downloads_hicexplorer| image:: https://img.shields.io/conda/dn/bioconda/hicexplorer.svg?style=flat :target: https://anaconda.org/bioconda/hicexplorer :alt: (downloads) .. |docker_hicexplorer| image:: https://quay.io/repository/biocontainers/hicexplorer/status :target: https://quay.io/repository/biocontainers/hicexplorer .. _`hicexplorer/tags`: https://quay.io/repository/biocontainers/hicexplorer?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/hicexplorer/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/hicexplorer/README.html