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Bioconductor - EpiCompare (development version)

EpiCompare

This is the development version of EpiCompare; for the stable release version, see EpiCompare.

Comparison, Benchmarking & QC of Epigenomic Datasets

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-5077-1984 , Brian Schilder [aut] ORCID: 0000-0001-5949-2191 , Leyla Abbasova [aut], Alan Murphy [aut] ORCID: 0000-0002-2487-8753 , Nathan Skene [aut] ORCID: 0000-0002-6807-3180 , Thomas Roberts [ctb], Hiranyamaya Dash [cre] ORCID: 0009-0005-5514-505X

Maintainer: Hiranyamaya Dash <hdash.work at gmail.com>

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

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

Details biocViews ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, Genetics, MultipleComparison, QualityControl, Software Version 1.13.0 In Bioconductor since BioC 3.15 (R-4.2) (3 years) License GPL-3 Depends R (>= 4.2.0) Imports AnnotationHub, ChIPseeker, data.table, genomation, GenomicRanges, IRanges(>= 2.41.3), 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 See More 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 Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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