About LOLA

Locus Overlap Analysis (LOLA) is an R Bioconductor package for genomic locus overlap enrichment. LOLA lets you test your genomic ranges of interest against a database of other genomic range sets to identify enrichment of overlap, tying external annotation to your regions of interest.

Region-set Databases

To test enrichments, you need a database. A good place to start is the LOLA Core database, which provides a curated resource of public datasets. You can also build your own problem-specific database of region sets. Collect internal or public sets of particular interest to you, and it’s very easy to build a custom database. Any newly generated region-set data can then be easily compared to your custom database. Information on both options are in the RegionDB docs.

Installing LOLA

LOLA is a Bioconductor package (since Oct 2015), and can be installed with:

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

The development version is maintained on GitHub and can be installed directly from github:

devtools::install_github("nsheff/LOLA")

Running LOLA

To start, follow the example in the manuscript (with example vignette data), or follow the more detailed R vignettes (also available in HTML at Bioconductor), illustrating how to get started, choose a universe, and use the LOLA Core database. It only takes a few lines of R code to run LOLA:

Feedback

Questions about how to use can be posted on Bioconductor Support, and bugs or feature requests should be filed as Github Issues.

Contributing

GitHub pull requests welcome.