EpiMix

DOI: 10.18129/B9.bioc.EpiMix  

EpiMix: an integrative tool for the population-level analysis of DNA methylation

Bioconductor version: Release (3.16)

EpiMix is a comprehensive tool for the integrative analysis of high-throughput DNA methylation data and gene expression data. EpiMix enables automated data downloading (from TCGA or GEO), preprocessing, methylation modeling, interactive visualization and functional annotation.To identify hypo- or hypermethylated CpG sites across physiological or pathological conditions, EpiMix uses a beta mixture modeling to identify the methylation states of each CpG probe and compares the methylation of the experimental group to the control group.The output from EpiMix is the functional DNA methylation that is predictive of gene expression. EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs.

Author: Yuanning Zheng [aut, cre], John Jun [aut], Olivier Gevaert [aut]

Maintainer: Yuanning Zheng <eric2021 at stanford.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("EpiMix")

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("EpiMix")

 

HTML	R Script	vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, GeneExpression, Preprocessing, Software
Version	1.0.1
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	GPL-3
Depends	R (>= 4.2.0), EpiMix.data(>= 0.99.2)
Imports	AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures, GenomicRanges, GEOquery, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils
LinkingTo
Suggests	BiocStyle, clusterProfiler, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
BugReports	https://github.com/gevaertlab/EpiMix/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	EpiMix_1.0.1.tar.gz
Windows Binary
macOS Binary (x86_64)	EpiMix_1.0.1.tgz
macOS Binary (arm64)	EpiMix_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EpiMix
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EpiMix
Bioc Package Browser	https://code.bioconductor.org/browse/EpiMix/
Package Short Url	https://bioconductor.org/packages/EpiMix/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive