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>

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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
Suggests testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick
URL https://github.com/GenEpi-GenPhySE/epistack
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