recipe bioconductor-epicompare

Comparison, Benchmarking & QC of Epigenomic Datasets






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.

package bioconductor-epicompare

(downloads) docker_bioconductor-epicompare



depends bioconductor-annotationhub:


depends bioconductor-biocgenerics:


depends bioconductor-brgenomics:


depends bioconductor-chipseeker:


depends bioconductor-genomation:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rtracklayer:


depends r-base:


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:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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<tag>

(see `bioconductor-epicompare/tags`_ for valid values for ``<tag>``)

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