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EpiDISH

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

Epigenetic Dissection of Intra-Sample-Heterogeneity

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Software
Version 2.17.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License GPL-2
Depends R (>= 4.1)
Imports MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix
Linking To
Suggests roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat
System Requirements
Enhances
URL https://github.com/sjczheng/EpiDISH
Bug Reports https://github.com/sjczheng/EpiDISH/issues
See More
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_2.17.0.tar.gz
Windows Binary EpiDISH_2.17.0.zip
macOS Binary (x86_64) EpiDISH_2.17.0.tgz
macOS Binary (arm64) EpiDISH_2.17.0.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