EpiCompare

DOI: 10.18129/B9.bioc.EpiCompare    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see EpiCompare.

Comparison, Benchmarking & QC of Epigenetic Datasets

Bioconductor version: 3.15

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.

Author: Sera Choi [aut, cre] , Brian Schilder [aut] , Alan Murphy [aut] , Nathan Skene [aut]

Maintainer: Sera Choi <serachoi1230 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EpiCompare")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("EpiCompare")

 

HTML	R Script	EpiCompare
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, Genetics, MultipleComparison, QualityControl, Software
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 years)
License	GPL-3
Depends	R (>= 4.1.0)
Imports	GenomicRanges, genomation, IRanges, reshape2, ggplot2, ChIPseeker, BRGenomics, clusterProfiler, plotly, stringr, dplyr, tidyr, UpSetR, rmarkdown, rtracklayer, AnnotationHub, utils, stats, methods, org.Hs.eg.db, S4Vectors, magrittr, plyranges
LinkingTo
Suggests	testthat (>= 3.0.0), badger, knitr, htmlwidgets, BiocStyle, data.table, BiocParallel, BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene
SystemRequirements
Enhances
URL	https://github.com/neurogenomics/EpiCompare
BugReports	https://github.com/neurogenomics/EpiCompare/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	EpiCompare_1.0.0.tar.gz
Windows Binary	EpiCompare_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	EpiCompare_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EpiCompare
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EpiCompare
Package Short Url	https://bioconductor.org/packages/EpiCompare/
Package Downloads Report	Download Stats