[Bioc-devel] New package: LOLA - Locus overlap analysis for enrichment of genomic ranges

[Nathan Sheffield]

We're pleased to announce the release of a new Bioconductor package, 
LOLA (Locus Overlap Analysis). LOLA is a package for genomic locus 
overlap enrichment. Roughly analogous to what GSEA does for gene sets, 
LOLA does for genomic regions, which can be defined however you like, 
including experiments like ChIP-seq, BS-seq, DNase-seq, etc. 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. A complete enrichment analysis 
against a database of thousands of region sets requires just 3 lines of 
R code and completes in minutes.

Along with LOLA, we provide the LOLA Core Database, which includes 
region sets from ENCODE, Roadmap Epigenomics, Cistrome, CODEX, UCSC, and 
other public databases. We intend to build, maintain, and curate this 
database over the coming years. You can also use LOLA for custom 
analysis by creating custom databases following instructions in the LOLA 
readme.

You can find more information, vignettes, and downloads at LOLA's 
website (http://databio.org/lola/), or follow our development at GitHub 
(https://github.com/sheffien/LOLA). We would be eager to hear any 
suggestions or feedback!

Nathan Sheffield and Christoph Bock