EpiDISH

DOI: 10.18129/B9.bioc.EpiDISH    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see EpiDISH.

Epigenetic Dissection of Intra-Sample-Heterogeneity

Bioconductor version: 3.9

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>

Installation

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

if (!requireNamespace("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")

 

HTML	R Script	Epigenetic Dissection of Intra-Sample-Heterogeneity
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Software
Version	2.0.2
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
License	GPL-2
Depends	R (>= 3.5)
Imports	MASS, e1071, quadprog, parallel, stats, matrixStats, stringr
LinkingTo
Suggests	roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat
SystemRequirements
Enhances
URL	https://github.com/sjczheng/EpiDISH
BugReports	https://github.com/sjczheng/EpiDISH/issues
Depends On Me
Imports Me
Suggests Me	FlowSorted.Blood.EPIC
Links To Me
Build Report

Package Archives

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

Source Package	EpiDISH_2.0.2.tar.gz
Windows Binary	EpiDISH_2.0.2.zip
Mac OS X 10.11 (El Capitan)	EpiDISH_2.0.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EpiDISH
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EpiDISH
Package Short Url	https://bioconductor.org/packages/EpiDISH/
Package Downloads Report	Download Stats