- recipe bioconductor-epicompare
Comparison, Benchmarking & QC of Epigenomic Datasets
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/EpiCompare.html
- License:
GPL-3
- Recipe:
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
- 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:
[](http://bioconda.github.io/recipes/bioconductor-epicompare/README.html)