EpiDISH

DOI: 10.18129/B9.bioc.EpiDISH    

This is the development version of EpiDISH; for the stable release version, see EpiDISH.

Epigenetic Dissection of Intra-Sample-Heterogeneity

Bioconductor version: Development (3.14)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	2.9.0
In Bioconductor since	BioC 3.6 (R-3.4) (4 years)
License	GPL-2
Depends	R (>= 4.1)
Imports	MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix
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	TOAST
Imports Me
Suggests Me	FlowSorted.Blood.EPIC, planet
Links To Me
Build Report

Package Archives

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

Source Package	EpiDISH_2.9.0.tar.gz
Windows Binary	EpiDISH_2.9.0.zip
macOS 10.13 (High Sierra)	EpiDISH_2.9.0.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