EpiDISH
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see EpiDISH.
Epigenetic Dissection of Intra-Sample-Heterogeneity
Bioconductor version: 3.11
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 "4.0") 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 | 2.4.0 |
| 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, locfdr |
| 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 | TOAST |
| 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_2.4.0.tar.gz |
| Windows Binary | EpiDISH_2.4.0.zip |
| macOS 10.13 (High Sierra) | EpiDISH_2.4.0.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 3.11 | Source Archive |