DOI: 10.18129/B9.bioc.epihet  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see epihet.

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Bioconductor version: 3.16

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>

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biocViews DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
Version 1.13.0
In Bioconductor since BioC 3.9 (R-3.6) (4 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
Suggests knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown
URL https://github.com/TheJacksonLaboratory/epihet
BugReports https://github.com/TheJacksonLaboratory/epihet/issues
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