EpiMix
EpiMix: an integrative tool for the population-level analysis of DNA methylation
Bioconductor version: Release (3.20)
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], Markus Sujansky [aut], John Jun [aut], Olivier Gevaert [aut]
Maintainer: Yuanning Zheng <eric2021 at stanford.edu>
citation("EpiMix")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, GeneExpression, Preprocessing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 years) |
| 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 |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/gevaertlab/EpiMix/issues |
See More
| Suggests | BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | Moonlight2R |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EpiMix_1.8.0.tar.gz |
| Windows Binary (x86_64) | EpiMix_1.8.0.zip |
| macOS Binary (x86_64) | EpiMix_1.8.0.tgz |
| macOS Binary (arm64) | EpiMix_1.7.1.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 |