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epigenomix

This is the development version of epigenomix; for the stable release version, see epigenomix.

Epigenetic and gene transcription data normalization and integration with mixture models


Bioconductor version: Development (3.19)

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 (from within R, enter citation("epigenomix")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF R Script
Reference Manual PDF

Details

biocViews ChIPSeq, Classification, DifferentialExpression, GeneExpression, Software
Version 1.43.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License LGPL-3
Depends R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment
Imports BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package epigenomix_1.43.0.tar.gz
Windows Binary epigenomix_1.43.0.zip (64-bit only)
macOS Binary (x86_64) epigenomix_1.43.0.tgz
macOS Binary (arm64) epigenomix_1.43.0.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