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regioneR

An R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association. regioneR is a customizable tool to manage and analyze sets of regions, and a useful addition to the NGS and genome wide analysis toolbox.

GINOM / Genomic INterval Overlap Model

Allows the interrogation of significant associations between many genomic features simultaneously. GINOM treats query interval location as a random variable of log-linear distribution with model terms formed from any possible combination, or interaction, of multiple reference sets. It can uncover any higher-order interaction among reference sets that has a significant effect on query interval location. It provides an effective method to screen for yet-uncharacterized higher-order associations between genomic features.

GenometriCorr / Genometric Correlation

A method for identifying whether two sets of intervals are spatially correlated across a genome, detected as a deviation from a nonuniform distribution of one set of intervals with respect to the other. GenometriCorr performs all analyses on each input, so that a variety of biologically significant relationships are queried. This includes looking for proximity, looking for uniform spacing, looking for increased or decreased overlaps of intervals or points, and presenting the data in a way that a biologist can understand.