Table 8.

Tools to Investigate Region Enrichement

	Languages	Notes	Docs	Citation
Annotatr	R	Annotate summarize and visualize genomic regions.	+++	Cavalcante & Sartor (2017) Last updated: 2019
BART/BARTweb	Python	Predict factors that bind at cis-regulatory regions.	+++	Wang et al. (2018) Last updated: 2020
chipenrich	R	Perform gene set enrichment testing using genomic regions.	+++	Welch et al. (2014) Last updated: 2020
coloc-stats	Python	Perform co-localization analysis of genomic regions.	+++	Simovski et al. (2018) Last updated: 2019
COLO	JSP	Identify genomic features in close proximity to user-submitted genomic regions.	++	Kim et al. (2015) Last updated: 2015
FEATnotator	Perl; R	Annotate genomic regions.	++	Podicheti & Mockaitis (2015) Last updated: 2018
GenomeRunner	.NET	Perform annotation and enrichment of genomic regions against default or custom regulatory regions.	++	Dozmorov et al. (2016) Last updated: 2016
GenometriCorr	R	Determine spatial correlation between region sets.	++	Favorov et al. (2012) Last updated: 2020
Genomic Association Tester	Python	Calculate the significance of overlaps between multiple genomic region sets.	+++	Heger et al. (2013) Last updated: 2019
GIGGLE	C	Genomics search engine to uncover significantly shared genomic loci (regions) between data.	+++	Layer et al. (2018) Last updated: 2019
GLANET	Java; Perl	Genomic loci annotation and enrichment tool between sets of genomic regions.	+++	Otlu et al. (2017) Last updated: 2019
GREAT	C	Annotate genomic regions.	+++	McLean et al. (2010) Last updated: 2019
LOLA/LOLAweb	R	Determine significant enrichment between region sets to inform on biological meaning.	+++	Sheffield & Bock (2016) Last updated: 2019
regioneR	R	Evaluate significant associations between region sets using permutation testing.	+++	Gel et al. (2016) Last updated: 2020
StereoGene	C++; R	Estimate genome-wide correlation between pairs of genomic features.	++	Stavrovskaya et al. (2017) Last updated: 2019