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Domain calling software tools | Hi-C data analysis

Topologically associating domains (TADs) have been proposed to be the basic unit of chromosome folding and have been shown to play key roles in genome organization and gene regulation.Source text:(Dali and Blanchette, 2017) A critical assessment of…
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Juicer
Desktop

Juicer

Analyzes terabase-scale Hi-C datasets. Juicer allows users without a…

Analyzes terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file…

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TopDom
Desktop

TopDom

Identifies topological domains (TDs), along with a set of statistical methods…

Identifies topological domains (TDs), along with a set of statistical methods for evaluating their quality. TopDom is more efficient than existing methods and depends on just one intuitive parameter:…

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TADtool
Desktop

TADtool Topologically Associating Domains tool

Finds robust TAD-calling parameters with immediate visual feedback. TADtool…

Finds robust TAD-calling parameters with immediate visual feedback. TADtool allows the direct export of TADs called with a chosen set of parameters for two of the most common TAD calling algorithms:…

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Arboretum-HiC
Desktop

Arboretum-HiC

A multi-task spectral clustering method, to identify common and…

A multi-task spectral clustering method, to identify common and context-specific aspects of genome architecture. Arboretum-Hi-C is based on a previous multi-task clustering approach, Arboretum, which…

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HiCExplorer
Desktop

HiCExplorer

Simplifies the Hi-C data pre-processing, contact matrix transformation, and…

Simplifies the Hi-C data pre-processing, contact matrix transformation, and topologically associating domain (TAD) calling into a few easy steps. HiCExplorer is a tool-suite that can be used with…

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HubPredictor
Desktop

HubPredictor

A computational model integrating Hi-C and histone mark ChIP-seq data to…

A computational model integrating Hi-C and histone mark ChIP-seq data to predict two important features of chromatin organization: chromatin interaction hubs and topologically associated domain (TAD)…

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TADtree
Desktop

TADtree

An algorithm for the identification of hierarchical topological domains in Hi-C…

An algorithm for the identification of hierarchical topological domains in Hi-C data. Beginning with contact matrix A, we compute the fold-enrichment over background for each pair of positions. For…

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HiCseg
Desktop

HiCseg

Detection of domains in HiC data. This package allows you to detect domains in…

Detection of domains in HiC data. This package allows you to detect domains in HiC data by rephrasing this problem as a two-dimensional segmentation issue.

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HiTAD
Desktop

HiTAD Hierarchical TAD

Recognizes hierarchical topologically associating domains (TADs) from Hi-C…

Recognizes hierarchical topologically associating domains (TADs) from Hi-C chromatin interactions. HiTAD was applied to analyzing Hi-C and in situ Hi-C datasets with different sequencing depths…

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Delta
Web
Desktop

Delta

Displays 3D structure of genome with diverse genomic features. Delta is a web…

Displays 3D structure of genome with diverse genomic features. Delta is a web based 3D genome visualization platform. This tool can be useful for researchers to infer novel and valid hypothesis via…

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TADLib
Desktop

TADLib

Detects hierarchical topologically associating domains (TADs) from Hi-C…

Detects hierarchical topologically associating domains (TADs) from Hi-C chromatin interactions. TADLib is an iterative optimization procedure that detects more hierarchical TADs than similar method…

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IC-Finder
Desktop

IC-Finder

Identifies interaction compartments (IC) from experimental Hi-C maps. IC-Finder…

Identifies interaction compartments (IC) from experimental Hi-C maps. IC-Finder is based on a hierarchical clustering approach that was adapted to account for the polymeric nature of chromatin. It…

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TADbit
Desktop

TADbit

Allows analysis and 3D modelling of 3C-based data. TADbit is a computational…

Allows analysis and 3D modelling of 3C-based data. TADbit is a computational framework including: (i) read quality control and design of the mapping strategy; (ii) mapping of reads to the reference…

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MrTADFinder
Desktop

MrTADFinder

Aims to identify topologically associating domains (TADs) from…

Aims to identify topologically associating domains (TADs) from intra-chromosomal contact maps. MrTADFinder is based on the concept of modularity. A key component is to derive a background model for…

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Armatus
Desktop

Armatus

Capturing persistent domains across various resolutions by adjusting a single…

Capturing persistent domains across various resolutions by adjusting a single scale parameter. Armatus produces domains that display much higher interaction frequencies within the domains than…

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