EpiCompare

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see EpiCompare.

Comparison, Benchmarking & QC of Epigenomic Datasets


Bioconductor version: 3.16

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>

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

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")
docker HTML R Script
EpiCompare HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, Genetics, MultipleComparison, QualityControl, Software
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (2 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
System Requirements
URL https://github.com/neurogenomics/EpiCompare
Bug Reports https://github.com/neurogenomics/EpiCompare/issues
See More
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
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Package Archives

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

Source Package EpiCompare_1.2.0.tar.gz
Windows Binary EpiCompare_1.2.0.zip (64-bit only)
macOS Binary (x86_64) EpiCompare_1.2.0.tgz
macOS Binary (arm64) EpiCompare_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/EpiCompare
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EpiCompare
Bioc Package Browser https://code.bioconductor.org/browse/EpiCompare/
Package Short Url https://bioconductor.org/packages/EpiCompare/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.16 Source Archive