:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-idr2d' .. highlight: bash bioconductor-idr2d ================== .. conda:recipe:: bioconductor-idr2d :replaces_section_title: :noindex: Irreproducible Discovery Rate for Genomic Interactions Data :homepage: https://bioconductor.org/packages/3.18/bioc/html/idr2d.html :license: MIT + file LICENSE :recipe: /`bioconductor-idr2d `_/`meta.yaml `_ A tool to measure reproducibility between genomic experiments that produce two\-dimensional peaks \(interactions between peaks\)\, such as ChIA\-PET\, HiChIP\, and HiC. idr2d is an extension of the original idr package\, which is intended for \(one\-dimensional\) ChIP\-seq peaks. .. conda:package:: bioconductor-idr2d |downloads_bioconductor-idr2d| |docker_bioconductor-idr2d| :versions: ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.2-0``,  ``1.0.0-0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-dplyr: ``>=0.7.6`` :depends r-futile.logger: ``>=1.4.3`` :depends r-ggplot2: ``>=3.1.1`` :depends r-idr: ``>=1.2`` :depends r-magrittr: ``>=1.5`` :depends r-reticulate: ``>=1.13`` :depends r-scales: ``>=1.0.0`` :depends r-stringr: ``>=1.3.1`` :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 bioconductor-idr2d and update with:: mamba update bioconductor-idr2d To create a new environment, run:: mamba create --name myenvname bioconductor-idr2d 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/bioconductor-idr2d: (see `bioconductor-idr2d/tags`_ for valid values for ````) .. |downloads_bioconductor-idr2d| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-idr2d.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-idr2d :alt: (downloads) .. |docker_bioconductor-idr2d| image:: https://quay.io/repository/biocontainers/bioconductor-idr2d/status :target: https://quay.io/repository/biocontainers/bioconductor-idr2d .. _`bioconductor-idr2d/tags`: https://quay.io/repository/biocontainers/bioconductor-idr2d?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/bioconductor-idr2d/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-idr2d/README.html