Package: epihet
Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Version: 1.0.0
Authors@R: c(person("Xiaowen", "Chen", role = c("aut", "cre"),
    email = "Xiaowen.Chen@jax.org"),
    person("Haitham", "Ashoor",role = "aut"),
    person("Ryan", "Musich", role = "aut"),
    person("Mingsheng","Zhang",role="aut"),
    person("Jiahui","Wang",role = "aut"),
    person("Sheng", "Li", role = "aut"))
Description: 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.
Depends:
    R(>= 3.6),
    GenomicRanges,
    IRanges,
    S4Vectors,
    ggplot2,
    foreach,
    Rtsne,
    igraph
License: Artistic-2.0
biocViews:
    DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
Imports:
    data.table,
    doParallel,
    EntropyExplorer,
    graphics,
    stats,
    grDevices,
    pheatmap,
    utils,
    qvalue,
    WGCNA,
    ReactomePA
Encoding: UTF-8
RoxygenNote: 6.0.1
Suggests:
    knitr,
    clusterProfiler,
    ggfortify,
    org.Hs.eg.db,
    rmarkdown
VignetteBuilder: knitr
BuildVignettes: TRUE
URL: https://github.com/TheJacksonLaboratory/epihet
BugReports: https://github.com/TheJacksonLaboratory/epihet/issues