epihet

DOI: 10.18129/B9.bioc.epihet    

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Bioconductor version: Release (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 (!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 1.2.0
In Bioconductor since BioC 3.9 (R-3.6) (0.5 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
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_1.2.0.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
Package Short Url https://bioconductor.org/packages/epihet/
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