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Data visualization software tools | Hi-C analysis

Efficient and accurate visualization of Hi-C data is not straightforward because Hi-C data is large and tools for the visualization of large-scale genomic data, such as genome browsers, do not directly generalize to visualizing data defined over…
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WashU…
Web

WashU Epigenome Browser

A genome browser focusing on the human epigenome. The Browser is web-based and…

A genome browser focusing on the human epigenome. The Browser is web-based and it extends the seminal concept invented by the UCSC Cancer Genomics Browser to support large, sequencing-based datasets.…

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my5C
Web

my5C

Provides an online 5C tool for the rapid design of 5C primers. my5C allows…

Provides an online 5C tool for the rapid design of 5C primers. my5C allows complete control over extremely complex 5C design schemes. This tool is composed of two modules. The “my5C.primers”…

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3DIV
Dataset

3DIV 3D Interaction Viewer and Database

Gathers a list of long-range chromatin interaction partners of any queried…

Gathers a list of long-range chromatin interaction partners of any queried locus. 3DIV allows exploration of long-range chromatin interaction patterns surrounding the target of interest and…

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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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Juicebox
Desktop

Juicebox

Explores Hi-C and other contact map data. Juicebox allows users to zoom in and…

Explores Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively. It integrates many technologies developed for the Integrative Genomics Viewer with a…

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HiCPlotter
Desktop

HiCPlotter

An easy-to-use open-source visualization tool to facilitate juxtaposition of…

An easy-to-use open-source visualization tool to facilitate juxtaposition of Hi-C matrices with diverse genomic assay outputs, as well as to compare interaction matrices between various conditions.…

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HiBrowse
Web

HiBrowse

A statistical web toolkit for analyzing, interpreting and visualizing…

A statistical web toolkit for analyzing, interpreting and visualizing genome-wide chromosome conformation capture data, such as Hi-C, TCC, GCC and similar.

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gcMapExplorer
Desktop

gcMapExplorer genome contact map explorer

Enables user to browse and analyze genome contact maps with reference to…

Enables user to browse and analyze genome contact maps with reference to genomic datasets. gcMapExplorer includes an interactive visualizer that facilitates the browsing of several contact maps…

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GrapHi-C
Desktop

GrapHi-C

Converts a normalized whole-genome contact map into an adjacency matrix.…

Converts a normalized whole-genome contact map into an adjacency matrix. GrapHi-C uses a graph-based representation of a whole-genome contact map and existing tools to more intuitively visualize Hi-C…

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BPS
Desktop

BPS BreakPoint Surveyor

Examines breakpoint predictions, together with their associated structural…

Examines breakpoint predictions, together with their associated structural variation and gene context. BPS is a pipeline for integrating large, complex data sets with a scalable architecture…

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HiView
Web

HiView

Leverages Hi-C results for the interpretation of Genome-wide association…

Leverages Hi-C results for the interpretation of Genome-wide association studies (GWAS) variants. HiView is able to display Hi-C data and statistical evidence for chromatin interactions in genomic…

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HUGIn
Web

HUGIn Hi­C Unifying Genomic Interrogator

Visualizes Hi-C data generated from 21 human primary tissues and cell liens.…

Visualizes Hi-C data generated from 21 human primary tissues and cell liens. HUGIn a web browser that enables assessment of chromatin contacts both constitutive across and specific to tissue(s)…

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Chorogenome…
Dataset

Chorogenome Navigator

Allows user to visualize high resolution Hi-C datasets, along with multiple…

Allows user to visualize high resolution Hi-C datasets, along with multiple other genomic features, like histone marks, chromatin states and motifs. Chorogenome Navigator is an interactive online…

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HiCPlus
Desktop

HiCPlus

Generates the high-resolution Hi-C interaction maps from low-resolution…

Generates the high-resolution Hi-C interaction maps from low-resolution interaction maps. HiCPlus is inspired by the most recent advancements in the single image super-resolution, which trains a…

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HiC-3DViewer
Web

HiC-3DViewer

Simplifies the 3D exploratory analysis of High Chromosome Contact map (Hi-C)…

Simplifies the 3D exploratory analysis of High Chromosome Contact map (Hi-C) data. HiC-3DViewer is an interactive chromatin visualization tool that maps genome-scale interactions to identify…

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hiCtools
Desktop

hiCtools

This collection of tools stream-lines the processing of HiC data from raw…

This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.

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3D Genome…
Web

3D Genome Browser

Allows users to visualize and explore chromatin interaction data, such as Hi-C,…

Allows users to visualize and explore chromatin interaction data, such as Hi-C, ChIA-PET, Capture Hi-C, PLAC-Seq, and more. 3D Genome Browser also allows users to browse other omics data such as…

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TADkit
Web
Desktop

TADkit

Produces interactive 3D representations of modelled chromatin conformations.…

Produces interactive 3D representations of modelled chromatin conformations. TADkit allows users to study the relationship between 3D structure of the genome and its biological function. This tool is…

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HiCBrowser
Desktop

HiCBrowser

Visualizes any gene or region in context of topologically associating domains…

Visualizes any gene or region in context of topologically associating domains (TADs). HiCBrowser is an underlying program freely available as a standalone, where users can include their own genomic…

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