epiRomics
This is the released version of epiRomics; for the devel version, see epiRomics.
Epigenomic Analysis Package Built for R (epiRomics)
Bioconductor version: Release (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")):
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")
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 | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, ChIPSeq, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, RNASeq, Sequencing, Software, Transcription, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | epiRomics_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | epiRomics_1.0.0.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 |