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EpiCompare

Comparison, Benchmarking & QC of Epigenomic Datasets

Bioconductor version: Release (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>

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

Installation

To install this package, start R (version "4.3") 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
example_report HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, Genetics, MultipleComparison, QualityControl, Software
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License GPL-3
Depends R (>= 4.2.0)
Imports AnnotationHub, BRGenomics, ChIPseeker, data.table, genomation, GenomicRanges, IRanges, GenomeInfoDb, ggplot2, htmltools, methods, plotly, reshape2, rmarkdown, rtracklayer, stats, stringr, utils, BiocGenerics, downloadthis, parallel
Linking To
Suggests rworkflows, BiocFileCache, BiocParallel, 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, ComplexUpset, plyranges, scales, Matrix, consensusSeekeR, heatmaply, viridis
System Requirements
Enhances
URL https://github.com/neurogenomics/EpiCompare
Bug Reports https://github.com/neurogenomics/EpiCompare/issues
See More
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_1.4.0.tar.gz
Windows Binary EpiCompare_1.3.0.zip (64-bit only)
macOS Binary (x86_64) EpiCompare_1.4.0.tgz
macOS Binary (arm64) EpiCompare_1.4.0.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