EpiDISH

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see EpiDISH.

Epigenetic Dissection of Intra-Sample-Heterogeneity

Bioconductor version: 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>

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

Installation

To install this package, start R (version "4.1") 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 2.10.0

In Bioconductor since BioC 3.6 (R-3.4) (6.5 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 FlowSorted.Blood.EPIC, planet

Links To Me

Build Report Build Report

Package Archives

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

Source Package EpiDISH_2.10.0.tar.gz

Windows Binary EpiDISH_2.10.0.zip

macOS 10.13 (High Sierra) EpiDISH_2.10.0.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

Old Source Packages for BioC 3.14 Source Archive