epistack
Heatmaps of Stack Profiles from Epigenetic Signals
Bioconductor version: Release (3.20)
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 | 1.12.0 |
| 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_1.12.0.tar.gz |
| Windows Binary (x86_64) | epistack_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | epistack_1.12.0.tgz |
| macOS Binary (arm64) | epistack_1.11.0.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 |