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DESCRIPTION
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DESCRIPTION
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Package: epistack
Title: Heatmaps of Stack Profiles from Epigenetic Signals
Version: 1.7.2
Authors@R: c(person("SACI", "Safia", email = "safiasaci1995@gmail.com", role = "aut"),
person("DEVAILLY", "Guillaume",
email = "gdevailly@hotmail.com", role = c("cre", "aut")))
Description: The epistack package main objective is the visualizations of
stacks of genomic tracks (such as, but not restricted to, ChIP-seq,
ATAC-seq, DNA methyation or genomic conservation data)
centered at genomic regions of interest. epistack needs three
different inputs: 1) a genomic score objects, such as ChIP-seq coverage or
DNA methylation values,
provided as a `GRanges` (easily obtained from `bigwig` or `bam` files).
2) a list of feature of interest, such as peaks or transcription start
sites, provided as a `GRanges` (easily obtained from `gtf` or `bed` files).
3) a score to sort the features, such as peak height or gene
expression value.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Imports:
GenomicRanges,
SummarizedExperiment,
BiocGenerics,
S4Vectors,
IRanges,
graphics,
plotrix,
grDevices,
stats,
methods
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
Depends:
R (>= 4.1)
Suggests:
testthat (>= 3.0.0),
BiocStyle,
knitr,
rmarkdown,
EnrichedHeatmap,
biomaRt,
rtracklayer,
covr,
vdiffr,
magick
Config/testthat/edition: 3
VignetteBuilder: knitr
biocViews: RNASeq, Preprocessing, ChIPSeq, GeneExpression, Coverage
URL: https://github.com/GenEpi-GenPhySE/epistack