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Genomic region enrichment analysis software tools | Genome annotation

Genomic datasets are often interpreted in the context of large-scale reference databases. One approach is to identify significantly overlapping gene sets, which works well for gene-centric data. However, many types of high-throughput data are based…
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GREAT
Web

GREAT

Predicts functions of cis-regulatory regions. Many coding genes are well…

Predicts functions of cis-regulatory regions. Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. GREAT assigns biological meaning…

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genomation
Desktop

genomation

An R package that contains a collection of tools for visualizing and analyzing…

An R package that contains a collection of tools for visualizing and analyzing genome-wide data sets. The package works with a variety of genomic interval file types and enables easy summarization…

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EpiGRAPH
Web

EpiGRAPH

Enables biologists to uncover hidden associations in vertebrate genome and…

Enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA…

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The Genomic…
Web

The Genomic HyperBrowser

A comprehensive system for statistical analysis of genomic tracks. Through the…

A comprehensive system for statistical analysis of genomic tracks. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the…

i-cisTarget
Web

i-cisTarget

An integrative genomics method for the prediction of regulatory features and…

An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly. ii-cisTarget enables: (i) to detect transcription factor motifs in a set…

ReMap
Web

ReMap

An integrative analysis of transcription factor ChIP-seq experiments publicly…

An integrative analysis of transcription factor ChIP-seq experiments publicly available merged with the Encode dataset. A full access to this catalogue is available online together with the TFs…

LOLA
Desktop

LOLA Location Overlap Analysis

A package for genomic locus overlap enrichment. Roughly analogous to what GSEA…

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…

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GIGGLE
Desktop

GIGGLE

Allows users to conduct large-scale comparisons of their results with thousands…

Allows users to conduct large-scale comparisons of their results with thousands of reference datasets and genome annotations in seconds. GIGGLE permits to identify novel and unexpected relationships…

GLANET
Desktop

GLANET Genomic Loci AssociatioN and Enrichment Tool

Offers useful features for performing flexible annotation and enrichment…

Offers useful features for performing flexible annotation and enrichment analysis of a given set of fixed or varying length loci. GLANET is an easy-to-run desktop and command line application that…

Genome Track…
Web

Genome Track Analyzer

Provides an efficient tool for the study of correlations between genome…

Provides an efficient tool for the study of correlations between genome features with useful applications to many genetic problems. The study of correlations between genome tracks may shed light on…

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ColoWeb
Web

ColoWeb

A web-based service for evaluating the colocation of genomic features. Users…

A web-based service for evaluating the colocation of genomic features. Users submit genomic regions of interest, for example, a set of locations from a ChIP-seq analysis. ColoWeb compares the…

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…

REEF
Desktop

REEF REgionally Enriched Features

Aims at the identification of genomic regions containing features locally…

Aims at the identification of genomic regions containing features locally clustered. REEF scans the considered genome using a sliding window approach and adopts the False Discovery Rate (FDR) to give…

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