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
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