EpiCompare
This is the development version of EpiCompare; for the stable release version, see EpiCompare.
Comparison, Benchmarking & QC of Epigenomic Datasets
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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_1.17.0.tar.gz |
| Windows Binary (x86_64) | EpiCompare_1.17.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | EpiCompare_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | EpiCompare_1.17.0.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/ |
| Package Downloads Report | Download Stats |