EpiCompare

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see EpiCompare.

Comparison, Benchmarking & QC of Epigenomic Datasets

Bioconductor version: 3.19

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] , Brian Schilder [aut] , Leyla Abbasova [aut], Alan Murphy [aut] , Thomas Roberts [cre], Nathan Skene [aut]

Maintainer: Thomas Roberts <tomroberts.work15 at gmail.com>

Citation (from within R, enter citation("EpiCompare")):

Installation

To install this package, start R (version "4.4") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, Genetics, MultipleComparison, QualityControl, Software
Version	1.8.1
In Bioconductor since	BioC 3.15 (R-4.2) (2.5 years)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	AnnotationHub, BRGenomics, ChIPseeker, data.table, genomation, GenomicRanges, IRanges, GenomeInfoDb, ggplot2 (>= 3.5.0), htmltools, methods, plotly, reshape2, rmarkdown, rtracklayer, stats, stringr, utils, BiocGenerics, downloadthis, parallel
System Requirements
URL	https://github.com/neurogenomics/EpiCompare
Bug Reports	https://github.com/neurogenomics/EpiCompare/issues

Suggests	rworkflows, BiocFileCache, BiocParallel, BiocStyle, clusterProfiler, GenomicAlignments, grDevices, 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, ComplexUpset, plyranges, scales, Matrix, consensusSeekeR, heatmaply, viridis
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
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