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 frombigwig
orbam
files) - a list of feature of interest, such as peaks or transcription start sites,
provided as a
GRanges
(easily obtained fromgtf
orbed
files) - a score to sort the features, such as peak height or gene expression value
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")
A version of epistack
vignette can be read here.
{epistack} recieved financial support from INRAE and from Agence Nationnale de la Recherche through the funding ANR-19-DATA-0007.