recipe bioconductor-epicompare

Comparison, Benchmarking & QC of Epigenomic Datasets

Homepage:

https://bioconductor.org/packages/3.16/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.

package bioconductor-epicompare

Versions:

1.2.0-0

Depends:

• bioconductor-annotationhub >=3.6.0,<3.7.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-brgenomics >=1.10.0,<1.11.0

• bioconductor-chipseeker >=1.34.0,<1.35.0

• bioconductor-genomation >=1.30.0,<1.31.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-ggplot2

• r-htmltools

• r-plotly

• r-reshape2

• r-rmarkdown

• r-stringr

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-epicompare

and update with:

conda update bioconductor-epicompare

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-epicompare:<tag>

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

Download stats

Link to this page

Render an 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)