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Genomic region overlap analysis software tools | Genome annotation

A common question in genomic analysis is whether two sets of genomic intervals overlap significantly. This question arises, for example, when interpreting ChIP-Seq or RNA-Seq data in functional terms. Because genome organization is complex,…
regioneR
Desktop

regioneR

An R package that implements a permutation test framework specifically designed…

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…

GINOM
Desktop

GINOM Genomic INterval Overlap Model

Allows the interrogation of significant associations between many genomic…

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…

MULTOVL
Desktop

MULTOVL

Allows users to distinguish and investigate multiple overlaps of genomic…

Allows users to distinguish and investigate multiple overlaps of genomic regions. MULTOVL is a suite of tools that contains: (i) MULTOVL for estimating overlap null distributions; (ii) MULTOVLPROB…

KLTepigenome
Desktop

KLTepigenome

Allows to explore and uncover patterns of epigenomic variability and…

Allows to explore and uncover patterns of epigenomic variability and covariability. KLTepigenome uses a functional data analysis approach based on the Karhunen-Loève transform. It can outperform…

StereoGene
Desktop

StereoGene

Estimates genome-wide positional correlations. StereoGene is able to rapidly…

Estimates genome-wide positional correlations. StereoGene is able to rapidly compute correlations of continuous genome-wide features in addition to discrete gene intervals used in most correlation…

GAT
Desktop

GAT Genomic Association Test

A tool for estimating the significance of overlap between multiple sets of…

A tool for estimating the significance of overlap between multiple sets of genomic intervals. GAT implements a null model that the two sets of intervals are placed independently of one another, but…

GenometriCorr
Desktop

GenometriCorr Genometric Correlation

A method for identifying whether two sets of intervals are spatially correlated…

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…

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