EpiCompare

Comparison, Benchmarking & QC of Epigenomic Datasets

Bioconductor version: 3.23 · Package version: 1.16.0

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.

Installation

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

BiocManager::install("EpiCompare")

Details

Maintainer	Hiranyamaya Dash <hdash.work@gmail.com>
Author	Sera Choi [aut] (ORCID: <https://orcid.org/0000-0002-5077-1984>), Brian Schilder [aut] (ORCID: <https://orcid.org/0000-0001-5949-2191>), Leyla Abbasova [aut], Alan Murphy [aut] (ORCID: <https://orcid.org/0000-0002-2487-8753>), Nathan Skene [aut] (ORCID: <https://orcid.org/0000-0002-6807-3180>), Thomas Roberts [ctb], Hiranyamaya Dash [cre] (ORCID: <https://orcid.org/0009-0005-5514-505X>)
License	GPL-3
URL	https://github.com/neurogenomics/EpiCompare
Bug Reports	https://github.com/neurogenomics/EpiCompare/issues
Downloads rank	261
Source branch	RELEASE_3_23
biocViews	ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, Genetics, MultipleComparison, QualityControl, Software

Documentation

Download

Source package

Dependencies

Depends: R (>= 4.2.0)

Imports: AnnotationHub, ChIPseeker, data.table, genomation, GenomicRanges, IRanges (>= 2.41.3), Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.7), ggplot2 (>= 3.5.0), htmltools, methods, plotly, reshape2, rmarkdown, rtracklayer, stats, stringr, utils, BiocGenerics, downloadthis, parallel

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