EpiDISH

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see EpiDISH.

Epigenetic Dissection of Intra-Sample-Heterogeneity

Bioconductor version: 3.19

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 [aut], Shijie C. Zheng [aut, cre]

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

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

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Software
Version	2.20.1
In Bioconductor since	BioC 3.6 (R-3.4) (7 years)
License	GPL-2
Depends	R (>= 4.1)
Imports	MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix
System Requirements
URL	https://github.com/sjczheng/EpiDISH
Bug Reports	https://github.com/sjczheng/EpiDISH/issues

Suggests	roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat
Linking To
Enhances
Depends On Me	TOAST
Imports Me
Suggests Me	planet
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	EpiDISH_2.20.1.tar.gz
Windows Binary (x86_64)	EpiDISH_2.20.1.zip (64-bit only)
macOS Binary (x86_64)	EpiDISH_2.20.1.tgz
macOS Binary (arm64)	EpiDISH_2.20.1.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 3.19	Source Archive