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]
, Brian Schilder [aut]
, Leyla Abbasova [aut], Alan Murphy [aut]
, Nathan Skene [aut]
, Thomas Roberts [ctb], Hiranyamaya Dash [cre]
Maintainer: Hiranyamaya Dash <hdash.work at gmail.com>
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")| docker | HTML | R Script |
| EpiCompare | HTML | R Script |
| example_report | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, Genetics, MultipleComparison, QualityControl, Software |
| Version | 1.13.2 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 years) |
| License | GPL-3 |
| 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 |
| 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.
| Source Package | EpiCompare_1.13.2.tar.gz |
| Windows Binary (x86_64) | EpiCompare_1.13.1.zip |
| macOS Binary (x86_64) | EpiCompare_1.13.2.tgz |
| macOS Binary (arm64) | EpiCompare_1.13.2.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 |