epihet

DOI: 10.18129/B9.bioc.epihet    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see epihet.

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF	R Script	epihet
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
Version	1.6.1
In Bioconductor since	BioC 3.9 (R-3.6) (2 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
LinkingTo
Suggests	knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/TheJacksonLaboratory/epihet
BugReports	https://github.com/TheJacksonLaboratory/epihet/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	epihet_1.6.1.tar.gz
Windows Binary	epihet_1.6.1.zip
macOS 10.13 (High Sierra)	epihet_1.6.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/epihet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/epihet
Package Short Url	https://bioconductor.org/packages/epihet/
Package Downloads Report	Download Stats