epiRomics
This is the development version of epiRomics; to use it, please install the devel version of Bioconductor.
Epigenomic Analysis Package Built for R (epiRomics)
Bioconductor version: Development (3.23)
Integrates various levels of epigenomic information, including ChIP-seq, histone modification, ATAC-seq, and RNA-seq data. Regulatory network analysis uses combinatory approaches to infer regions of significance, such as enhancers. Downstream analysis identifies co-occurrence of epigenomic data at regions of interest. Visualization functions display multi-track genomic views with signal overlays. Please contact
Author: Alex M. Mawla [aut, cre]
, Mark O. Huising [aut]
Maintainer: Alex M. Mawla <ammawla at ucdavis.edu>
citation("epiRomics")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("epiRomics")
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("epiRomics")| Getting Started with epiRomics | HTML | R Script |
| Reference Manual |
Details
| biocViews | ATACSeq, ChIPSeq, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, RNASeq, Sequencing, Software, Transcription, Visualization |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | AnnotationDbi(>= 1.68.0), annotatr(>= 1.32.0), BiocGenerics(>= 0.52.0), ChIPseeker(>= 1.42.0), data.table (>= 1.15.0), digest (>= 0.6.35), GenomeInfoDb(>= 1.42.0), GenomicFeatures(>= 1.58.0), GenomicRanges(>= 1.58.0), graphics, grDevices, IRanges(>= 2.40.0), methods, rtracklayer(>= 1.66.0), S4Vectors(>= 0.44.0), stats, tools, utils |
| System Requirements | |
| URL | https://huising-lab.github.io/epiRomics/ https://github.com/Huising-Lab/epiRomics |
| Bug Reports | https://github.com/Huising-Lab/epiRomics/issues |
See More
| Suggests | BiocFileCache(>= 2.14.0), knitr, org.Hs.eg.db(>= 3.20.0), org.Mm.eg.db(>= 3.20.0), parallel, rmarkdown, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene(>= 3.18.0), TxDb.Mmusculus.UCSC.mm10.knownGene(>= 3.10.0) |
| 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 | epiRomics_0.99.5.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | epiRomics_0.99.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/epiRomics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/epiRomics |
| Bioc Package Browser | https://code.bioconductor.org/browse/epiRomics/ |
| Package Short Url | https://bioconductor.org/packages/epiRomics/ |
| Package Downloads Report | Download Stats |