README.md

In GenEpi-GenPhySE/epistack: Heatmaps of Stack Profiles from Epigenetic Signals

epistack

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:

• a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a GRanges (easily obtained from bigwig or bam files)
• a list of feature of interest, such as peaks or transcription start sites, provided as a GRanges (easily obtained from gtf or bed files)
• a score to sort the features, such as peak height or gene expression value

Installation

To install the package from Bioconductor, use:

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

BiocManager::install("epistack")

You can install the GitHub version of epistack from R using :

remotes::install_github("GenEpi-GenPhySE/epistack")

Documentation

A version of epistack vignette can be read here.

Funding

{epistack} recieved financial support from INRAE and from Agence Nationnale de la Recherche through the funding ANR-19-DATA-0007.

GenEpi-GenPhySE/epistack documentation built on July 27, 2023, 1:09 a.m.