epigenomix
This is the released version of epigenomix; for the devel version, see epigenomix.
Epigenetic and gene transcription data normalization and integration with mixture models
Bioconductor version: Release (3.23)
A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.
Author: Hans-Ulrich Klein, Martin Schaefer
Maintainer: Hans-Ulrich Klein <h.klein at uni-muenster.de>
citation("epigenomix")):
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("epigenomix")
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("epigenomix")| epigenomix package vignette | R Script | |
| Reference Manual |
Details
| biocViews | ChIPSeq, Classification, DifferentialExpression, GeneExpression, Software |
| Version | 1.52.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | LGPL-3 |
| Depends | R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment |
| Imports | BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray |
| System Requirements | |
| URL |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | epigenomix_1.52.0.tar.gz |
| Windows Binary (x86_64) | epigenomix_1.52.0.zip |
| macOS Binary (big-sur-x86_64) | epigenomix_1.52.0.tgz |
| macOS Binary (sonoma-arm64) | epigenomix_1.52.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/epigenomix |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/epigenomix |
| Bioc Package Browser | https://code.bioconductor.org/browse/epigenomix/ |
| Package Short Url | https://bioconductor.org/packages/epigenomix/ |
| Package Downloads Report | Download Stats |