:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'r-shaman' .. highlight: bash r-shaman ======== .. conda:recipe:: r-shaman :replaces_section_title: :noindex: The shaman package \- sampling HiC contact matrices for a\-parametric normalization :homepage: https://tanaylab.github.io/shaman/ :license: GPL :recipe: /`r-shaman `_/`meta.yaml `_ .. conda:package:: r-shaman |downloads_r-shaman| |docker_r-shaman| :versions: ``2.0-6``,  ``2.0-5``,  ``2.0-4``,  ``2.0-1``,  ``2.0-0`` :depends bioconductor-genomeinfodb: :depends bioconductor-gviz: :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-domc: :depends r-misha: :depends r-plyr: :depends r-rann: :depends r-reshape2: :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 r-shaman and update with:: mamba update r-shaman To create a new environment, run:: mamba create --name myenvname r-shaman 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/r-shaman: (see `r-shaman/tags`_ for valid values for ````) .. |downloads_r-shaman| image:: https://img.shields.io/conda/dn/bioconda/r-shaman.svg?style=flat :target: https://anaconda.org/bioconda/r-shaman :alt: (downloads) .. |docker_r-shaman| image:: https://quay.io/repository/biocontainers/r-shaman/status :target: https://quay.io/repository/biocontainers/r-shaman .. _`r-shaman/tags`: https://quay.io/repository/biocontainers/r-shaman?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/r-shaman/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/r-shaman/README.html