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EpiMix

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

Bioconductor version: Release (3.17)

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>

Citation (from within R, enter citation("EpiMix")):

Installation

To install this package, start R (version "4.3") 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")
vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, GeneExpression, Preprocessing, Software
Version 1.2.4
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License GPL-3
Depends R (>= 4.2.0), EpiMix.data(>= 1.2.2)
Imports AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils
Linking To
Suggests BiocStyle, clusterProfiler, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter
System Requirements
Enhances
URL
Bug Reports https://github.com/gevaertlab/EpiMix/issues
See More
Depends On Me
Imports Me
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Build Report  

Package Archives

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

Source Package EpiMix_1.2.4.tar.gz
Windows Binary EpiMix_1.2.4.zip (64-bit only)
macOS Binary (x86_64) EpiMix_1.2.4.tgz
macOS Binary (arm64)
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 3.17 Source Archive