epistack

DOI: 10.18129/B9.bioc.epistack  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see epistack.

Heatmaps of Stack Profiles from Epigenetic Signals

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	Using epistack
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ChIPSeq, Coverage, GeneExpression, Preprocessing, RNASeq, Software
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	MIT + file LICENSE
Depends	R (>= 4.1)
Imports	GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods
LinkingTo
Suggests	testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick
SystemRequirements
Enhances
URL	https://github.com/GenEpi-GenPhySE/epistack
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	epistack_1.6.0.tar.gz
Windows Binary	epistack_1.6.0.zip
macOS Binary (x86_64)	epistack_1.6.0.tgz
macOS Binary (arm64)	epistack_1.6.0.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