epihet

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.17 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: 3.17

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 "4.3") 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

Reference Manual PDF

Details

biocViews DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
Version 1.16.0
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
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Suggests knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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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Old Source Packages for BioC 3.17 Source Archive