EpiCompare

DOI: 10.18129/B9.bioc.EpiCompare    

This is the development version of EpiCompare; for the stable release version, see EpiCompare.

Comparison, Benchmarking & QC of Epigenomic Datasets

Bioconductor version: Development (3.17)

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] , Leyla Abbasova [aut], Alan Murphy [aut] , Nathan Skene [aut]

Maintainer: Sera Choi <serachoi1230 at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	docker
HTML	R Script	EpiCompare
PDF		Reference Manual

Details

biocViews	ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, Genetics, MultipleComparison, QualityControl, Software
Version	1.3.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 years)
License	GPL-3
Depends	R (>= 4.1.0)
Imports	AnnotationHub, BRGenomics, ChIPseeker, data.table, genomation, GenomicRanges, IRanges, GenomeInfoDb, ggplot2, htmltools, methods, plotly, reshape2, rmarkdown, rtracklayer, stats, stringr, utils, BiocGenerics
LinkingTo
Suggests	badger, BiocFileCache, BiocParallel, parallel, BiocStyle, clusterProfiler, GenomicAlignments, grDevices, htmlwidgets, knitr, org.Hs.eg.db, testthat (>= 3.0.0), tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, UpSetR, plyranges, scales, Matrix, consensusSeekeR
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_1.3.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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