:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-epicompare' .. highlight: bash bioconductor-epicompare ======================= .. conda:recipe:: bioconductor-epicompare :replaces_section_title: :noindex: Comparison\, Benchmarking \& QC of Epigenomic Datasets :homepage: https://bioconductor.org/packages/3.17/bioc/html/EpiCompare.html :license: GPL-3 :recipe: /`bioconductor-epicompare `_/`meta.yaml `_ EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections\: \(1. General metrics\) Metrics on peaks \(percentage of blacklisted and non\-standard peaks\, and peak widths\) and fragments \(duplication rate\) of samples\, \(2. Peak overlap\) Percentage and statistical significance of overlapping and non\-overlapping peaks. Also includes upset plot and \(3. Functional annotation\) functional annotation \(ChromHMM\, ChIPseeker and enrichment analysis\) of peaks. Also includes peak enrichment around TSS. .. conda:package:: bioconductor-epicompare |downloads_bioconductor-epicompare| |docker_bioconductor-epicompare| :versions: ``1.4.0-0``,  ``1.2.0-0`` :depends bioconductor-annotationhub: ``>=3.8.0,<3.9.0`` :depends bioconductor-biocgenerics: ``>=0.46.0,<0.47.0`` :depends bioconductor-brgenomics: ``>=1.12.0,<1.13.0`` :depends bioconductor-chipseeker: ``>=1.36.0,<1.37.0`` :depends bioconductor-genomation: ``>=1.32.0,<1.33.0`` :depends bioconductor-genomeinfodb: ``>=1.36.0,<1.37.0`` :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 r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: :depends r-downloadthis: :depends r-ggplot2: :depends r-htmltools: :depends r-plotly: :depends r-reshape2: :depends r-rmarkdown: :depends r-stringr: :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-epicompare and update with:: mamba update bioconductor-epicompare To create a new environment, run:: mamba create --name myenvname bioconductor-epicompare 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-epicompare: (see `bioconductor-epicompare/tags`_ for valid values for ````) .. |downloads_bioconductor-epicompare| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-epicompare.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-epicompare :alt: (downloads) .. |docker_bioconductor-epicompare| image:: https://quay.io/repository/biocontainers/bioconductor-epicompare/status :target: https://quay.io/repository/biocontainers/bioconductor-epicompare .. _`bioconductor-epicompare/tags`: https://quay.io/repository/biocontainers/bioconductor-epicompare?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-epicompare/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-epicompare/README.html