LOLAweb

LOLAweb is a web server and interactive results viewer for enrichment of overlap between a query region set (a bed file) and a database of region sets. It provides an interactive result explorer to visualize the highest ranked enrichments from the database. You can access the web server at http://lolaweb.databio.org

LOLAweb is an interactive application that implements functions from the LOLA package in a web interface via the Shiny framework.

The app is hosted and available for use at:

http://lolaweb.databio.org

To run the application locally, you’ll need to first clone this repository:

git clone https://github.com/databio/LOLAweb.git

The app requires R to be installed, as well as several packages. From within R run the following to install the dependencies:

install.packages(c("ggplot2", "shiny", "DT", "shinyWidgets", "shinyjs", "sodium", "devtools", "shinyBS"))
devtools::install_github("databio/simpleCache")
devtools::install_github("databio/GenomicDistributions")

source("https://bioconductor.org/biocLite.R")
biocLite(c("LOLA", "GenomicRanges"))

You’ll also need underlying data that is not available in this repository in order to establish the universes, example user sets and reference genome directories. Run the following from within the root of this folder to download the data and create the universes/, userSets/, reference/ and cache/ directories respectively:

# create universes dir
mkdir universes
mkdir userSets

# example universe and user set
curl http://cloud.databio.org.s3.amazonaws.com/vignettes/lola_vignette_data_150505.tgz | tar xvz

mv lola_vignette_data/activeDHS_universe.bed universes/.
mv lola_vignette_data/setB_100.bed userSets/.

rm -rf lola_vignette_data
# create reference dir
mkdir reference

# core
curl http://cloud.databio.org.s3.amazonaws.com/regiondb/LOLACoreCaches_170206.tgz | tar xvz
mv scratch/ns5bc/resources/regions/LOLACore reference/Core
rm -rf scratch

# extended
curl http://cloud.databio.org.s3.amazonaws.com/regiondb/LOLAExtCaches_170206.tgz | tar xvz
mv scratch/ns5bc/resources/regions/LOLAExt reference/Extended
rm -rf scratch
# create cache dir
mkdir cache

With all of the above installed you can now launch the app with shiny::runApp() from within R at the root of this directory.