DOI: 10.18129/B9.bioc.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")):


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biocViews ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, Genetics, MultipleComparison, QualityControl, Software
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
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
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
URL https://github.com/neurogenomics/EpiCompare
BugReports https://github.com/neurogenomics/EpiCompare/issues
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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/
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