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This is the development version of EpiCompare; for the stable release version, see EpiCompare.
Bioconductor version: Development (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")
):
To install this package, start R (version "4.3") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("EpiCompare")
HTML | R Script | docker |
HTML | R Script | EpiCompare |
Reference Manual |
biocViews | ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, Genetics, MultipleComparison, QualityControl, Software |
Version | 1.3.0 |
In Bioconductor since | BioC 3.15 (R-4.2) (0.5 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 |
LinkingTo | |
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 |
SystemRequirements | |
Enhances | |
URL | https://github.com/neurogenomics/EpiCompare |
BugReports | https://github.com/neurogenomics/EpiCompare/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | EpiCompare_1.3.0.tar.gz |
Windows Binary | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/EpiCompare |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/EpiCompare |
Package Short Url | https://bioconductor.org/packages/EpiCompare/ |
Package Downloads Report | Download Stats |
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