This repository contains the code for the interactive browser of EpiMap data resource.

The project's main site can be found at compbio.mit.edu/epimap.

You can run the browser directly on your computer using the code in this repository and the shiny library in R as follows:

# Install shiny and other required packages:
pkgs = c('cba', 'DT', 'heatmaply', 'igraph', 'markdown', 'RColorBrewer', 
        'shiny', 'shinycssloaders', 'shinydashboard', 'shinyjs', 'shinythemes', 'shinyTree', 'shinyWidgets',
        'stringr', 'tidyr', 'visNetwork')

# Check for missing packages:
new.pkgs <- pkgs[!(pkgs %in% installed.packages()[,"Package"])]

# Install the missing packages:
if (length(new.pkgs)) install.packages(new.pkgs, dependencies=TRUE)

# Download and run the app from github:
library(shiny)
runGitHub("epimap_vis", "cboix")

In addition, we have manuscript analysis code on github at https://github.com/cboix/epimap_analysis

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Manuscript: Adsera et. al bioRxiv (2019) - Integrative analysis of 10,000 epigenomic maps across 800 samples for regulatory genomics and disease dissection