:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-chromswitch' .. highlight: bash bioconductor-chromswitch ======================== .. conda:recipe:: bioconductor-chromswitch :replaces_section_title: :noindex: An R package to detect chromatin state switches from epigenomic data :homepage: https://bioconductor.org/packages/3.17/bioc/html/chromswitch.html :license: MIT + file LICENSE :recipe: /`bioconductor-chromswitch `_/`meta.yaml `_ Chromswitch implements a flexible method to detect chromatin state switches between samples in two biological conditions in a specific genomic region of interest given peaks or chromatin state calls from ChIP\-seq data. .. conda:package:: bioconductor-chromswitch |downloads_bioconductor-chromswitch| |docker_bioconductor-chromswitch| :versions: .. raw:: html
1.22.0-01.20.0-01.16.0-01.14.0-01.12.0-11.12.0-01.10.0-01.8.0-01.6.0-1 ``1.22.0-0``,  ``1.20.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.4.1-0``,  ``1.4.0-0`` .. raw:: html
:depends bioconductor-biobase: ``>=2.60.0,<2.61.0`` :depends bioconductor-biocparallel: ``>=1.34.0,<1.35.0`` :depends bioconductor-genomicranges: ``>=1.52.0,<1.53.0`` :depends bioconductor-iranges: ``>=2.34.0,<2.35.0`` :depends bioconductor-rtracklayer: ``>=1.60.0,<1.61.0`` :depends bioconductor-s4vectors: ``>=0.38.0,<0.39.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-cluster: ``>=2.0.6`` :depends r-dplyr: ``>=0.5.0`` :depends r-gplots: ``>=3.0.1`` :depends r-lazyeval: ``>=0.2.0`` :depends r-magrittr: ``>=1.5`` :depends r-matrixstats: ``>=0.52`` :depends r-nmf: ``>=0.20.6`` :depends r-tidyr: ``>=0.6.3`` :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-chromswitch and update with:: mamba update bioconductor-chromswitch To create a new environment, run:: mamba create --name myenvname bioconductor-chromswitch 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-chromswitch: (see `bioconductor-chromswitch/tags`_ for valid values for ````) .. |downloads_bioconductor-chromswitch| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-chromswitch.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-chromswitch :alt: (downloads) .. |docker_bioconductor-chromswitch| image:: https://quay.io/repository/biocontainers/bioconductor-chromswitch/status :target: https://quay.io/repository/biocontainers/bioconductor-chromswitch .. _`bioconductor-chromswitch/tags`: https://quay.io/repository/biocontainers/bioconductor-chromswitch?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-chromswitch/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-chromswitch/README.html