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>
citation("EpiDISH")
):
Installation
To install this package, start R (version "3.6") 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 | ||
NEWS | Text |
Details
biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Software |
Version | 2.0.2 |
In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
License | GPL-2 |
Depends | R (>= 3.5) |
Imports | MASS, e1071, quadprog, parallel, stats, matrixStats, stringr |
System Requirements | |
URL | https://github.com/sjczheng/EpiDISH |
Bug Reports | https://github.com/sjczheng/EpiDISH/issues |
See More
Suggests | roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | FlowSorted.Blood.EPIC |
Links To Me | |
Build Report | 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 |
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 3.9 | Source Archive |