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epistack

This is the development version of epistack; for the stable release version, see epistack.

Heatmaps of Stack Profiles from Epigenetic Signals


Bioconductor version: Development (3.19)

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.

Author: SACI Safia [aut], DEVAILLY Guillaume [cre, aut]

Maintainer: DEVAILLY Guillaume <gdevailly at hotmail.com>

Citation (from within R, enter citation("epistack")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("epistack")

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("epistack")
Using epistack HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ChIPSeq, Coverage, GeneExpression, Preprocessing, RNASeq, Software
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods
System Requirements
URL https://github.com/GenEpi-GenPhySE/epistack
See More
Suggests testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package epistack_1.9.0.tar.gz
Windows Binary epistack_1.9.0.zip (64-bit only)
macOS Binary (x86_64) epistack_1.9.0.tgz
macOS Binary (arm64) epistack_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/epistack
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/epistack
Bioc Package Browser https://code.bioconductor.org/browse/epistack/
Package Short Url https://bioconductor.org/packages/epistack/
Package Downloads Report Download Stats