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Package: epihet
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Title: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
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Version: 1.0.0
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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"),
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person("Mingsheng","Zhang",role="aut"),
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person("Jiahui","Wang",role = "aut"),
person("Sheng", "Li", role = "aut"))
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Description: epihet is an R-package that calculates the epigenetic
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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
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the samples.epihet can be used to perform analysis on the data by creating
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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:
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R(>= 3.6),
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GenomicRanges,
IRanges,
S4Vectors,
ggplot2,
foreach,
Rtsne,
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igraph
License: Artistic-2.0
biocViews:
DNAMethylation, Epigenetics, MethylSeq, Sequencing, Software
Imports:
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data.table,
doParallel,
EntropyExplorer,
graphics,
stats,
grDevices,
pheatmap,
utils,
qvalue,
WGCNA,
ReactomePA
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Encoding: UTF-8
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RoxygenNote: 6.0.1
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Suggests:
knitr,
clusterProfiler,
ggfortify,
org.Hs.eg.db,
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rmarkdown
VignetteBuilder: knitr
BuildVignettes: TRUE
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URL: https://github.com/TheJacksonLaboratory/epihet
BugReports: https://github.com/TheJacksonLaboratory/epihet/issues
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