EpiDISH
This is the released version of EpiDISH; for the devel version, see EpiDISH.
Epigenetic Dissection of Intra-Sample-Heterogeneity
Bioconductor version: Release (3.23)
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 blood-tissue of any age, from birth to old-age, 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("EpiDISH")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 2.28.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | GPL-2 |
| Depends | R (>= 4.1) |
| Imports | MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix, genefilter |
| 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 | planet, CimpleG |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EpiDISH_2.28.0.tar.gz |
| Windows Binary (x86_64) | EpiDISH_2.28.0.zip |
| macOS Binary (big-sur-x86_64) | EpiDISH_2.28.0.tgz |
| macOS Binary (sonoma-arm64) | EpiDISH_2.28.0.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 |