epihet
This package is for version 3.9 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: 3.9
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("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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software |
| Version | 1.0.0 |
| 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 |
See More
| 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_1.0.0.tar.gz |
| Windows Binary | epihet_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | epihet_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/epihet |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |