epihet

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see epihet.

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Bioconductor version: 3.10

epihet is an R-package that calculates the epigenetic heterogeneity between cancer cells and/or normal cells. The functions establish a pipeline that take in bisulfite sequencing data from multiple samples and use the data to track similarities and differences in epipolymorphism,proportion of discordantly methylated sequencing reads (PDR),and Shannon entropy values at epialleles that are shared between the samples.epihet can be used to perform analysis on the data by creating pheatmaps, box plots, PCA plots, and t-SNE plots. MA plots can also be created by calculating the differential heterogeneity of the samples. And we construct co-epihet network and perform network analysis.

Author: Xiaowen Chen [aut, cre], Haitham Ashoor [aut], Ryan Musich [aut], Mingsheng Zhang [aut], Jiahui Wang [aut], Sheng Li [aut]

Maintainer: Xiaowen Chen <Xiaowen.Chen at jax.org>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("epihet")

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("epihet")

epihet	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.9 (R-3.6) (5 years)
License	Artistic-2.0
Depends	R (>= 3.6), GenomicRanges, IRanges, S4Vectors, ggplot2, foreach, Rtsne, igraph
Imports	data.table, doParallel, EntropyExplorer, graphics, stats, grDevices, pheatmap, utils, qvalue, WGCNA, ReactomePA
System Requirements
URL	https://github.com/TheJacksonLaboratory/epihet
Bug Reports	https://github.com/TheJacksonLaboratory/epihet/issues

Suggests	knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	epihet_1.2.0.tar.gz
Windows Binary	epihet_1.2.0.zip
Mac OS X 10.11 (El Capitan)	epihet_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/epihet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/epihet
Bioc Package Browser	https://code.bioconductor.org/browse/epihet/
Package Short Url	https://bioconductor.org/packages/epihet/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.10	Source Archive