epistack
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see epistack.
Heatmaps of Stack Profiles from Epigenetic Signals
Bioconductor version: 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("epistack")
):
Installation
To install this package, start R (version "4.4") 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")
Using epistack | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | ChIPSeq, Coverage, GeneExpression, Preprocessing, RNASeq, Software |
Version | 1.10.0 |
In Bioconductor since | BioC 3.14 (R-4.1) (3 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 |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | epistack_1.10.0.tar.gz |
Windows Binary (x86_64) | epistack_1.10.0.zip |
macOS Binary (x86_64) | epistack_1.10.0.tgz |
macOS Binary (arm64) | epistack_1.10.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/epistack |
Source Repository (Developer Access) | git clone [email protected]:packages/epistack |
Bioc Package Browser | https://code.bioconductor.org/browse/epistack/ |
Package Short Url | https://bioconductor.org/packages/epistack/ |
Package Downloads Report | Download Stats |