EpiDISH

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see EpiDISH.

Epigenetic Dissection of Intra-Sample-Heterogeneity


Bioconductor version: 3.10

EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of whole blood, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.

Author: Andrew E. Teschendorff <a.teschendorff at ucl.ac.uk>, Shijie C. Zheng<shijieczheng at gmail.com>

Maintainer: Shijie Charles Zheng<shijieczheng at gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("EpiDISH")

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("EpiDISH")
Epigenetic Dissection of Intra-Sample-Heterogeneity HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Software
Version 2.2.2
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-2
Depends R (>= 3.5)
Imports MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr
System Requirements
URL https://github.com/sjczheng/EpiDISH
Bug Reports https://github.com/sjczheng/EpiDISH/issues
See More
Suggests roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat
Linking To
Enhances
Depends On Me TOAST
Imports Me
Suggests Me FlowSorted.Blood.EPIC
Links To Me
Build Report Build Report

Package Archives

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

Source Package EpiDISH_2.2.2.tar.gz
Windows Binary EpiDISH_2.2.2.zip
Mac OS X 10.11 (El Capitan) EpiDISH_2.2.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/EpiDISH
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EpiDISH
Bioc Package Browser https://code.bioconductor.org/browse/EpiDISH/
Package Short Url https://bioconductor.org/packages/EpiDISH/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive