:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-medips' .. highlight: bash bioconductor-medips =================== .. conda:recipe:: bioconductor-medips :replaces_section_title: :noindex: DNA IP\-seq data analysis :homepage: https://bioconductor.org/packages/3.18/bioc/html/MEDIPS.html :license: GPL (>=2) :recipe: /`bioconductor-medips `_/`meta.yaml `_ :links: biotools: :biotools:`medips` MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation \(MeDIP\) experiments followed by sequencing \(MeDIP\-seq\). However\, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data \(e.g. ChIP\-seq\, MBD\-seq\, CMS\-seq and others\) including calculation of differential coverage between groups of samples and saturation and correlation analysis. .. conda:package:: bioconductor-medips |downloads_bioconductor-medips| |docker_bioconductor-medips| :versions: .. raw:: html
1.54.0-01.52.0-01.50.0-01.46.0-01.44.0-01.42.0-11.42.0-01.40.0-01.38.0-0 ``1.54.0-0``,  ``1.52.0-0``,  ``1.50.0-0``,  ``1.46.0-0``,  ``1.44.0-0``,  ``1.42.0-1``,  ``1.42.0-0``,  ``1.40.0-0``,  ``1.38.0-0``,  ``1.36.0-1``,  ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.24.0-0`` .. raw:: html
:depends bioconductor-biomart: ``>=2.58.0,<2.59.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0`` :depends bioconductor-dnacopy: ``>=1.76.0,<1.77.0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-preprocesscore: ``>=1.64.0,<1.65.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-gtools: :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-medips and update with:: mamba update bioconductor-medips To create a new environment, run:: mamba create --name myenvname bioconductor-medips 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-medips: (see `bioconductor-medips/tags`_ for valid values for ````) .. |downloads_bioconductor-medips| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-medips.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-medips :alt: (downloads) .. |docker_bioconductor-medips| image:: https://quay.io/repository/biocontainers/bioconductor-medips/status :target: https://quay.io/repository/biocontainers/bioconductor-medips .. _`bioconductor-medips/tags`: https://quay.io/repository/biocontainers/bioconductor-medips?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-medips/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-medips/README.html