3DGenomes/TADkit ↗
Created Dec 22, 2020 · View the 3DGenomes/TADkit repository page
3D Genome Browser
An animated visualization of 3DGenomes/TADkit's Git history from August 2014 to January 2020, built by 7 contributors. The codebase reached 10,396 lines, mostly JavaScript. The video runs 1 minute 45 seconds.
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Contributors
7
Lines of Code
10,396
From
Aug 17, 2014
To
Jan 29, 2020
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About 3DGenomes/TADkit
TADkit is a browser-based 3D genome visualization tool that allows researchers to explore the three-dimensional structure of chromatin and relate it to genomic function. Built with HTML5 and JavaScript, it combines D3.js for rendering one and two-dimensional genomic tracks with Three.js WebGL rendering for interactive 3D visualization. The tool was developed at the Marcinus Lab and creates interactive 3D models from 3C-based chromatin interaction matrices, enabling users to directly examine how genome structure correlates with biological processes.
The workflow involves three main steps: importing TADbit JSON files containing 3D chromatin models, selecting a specific cluster from an ensemble view, and analyzing the centroid model alongside genomic data. Users can overlay multiple data types including genes fetched from the Ensembl API, restraint graphs from the modeling process, and custom genomic tracks in BigWig or BedGraph formats. The interface displays the 3D chromatin structure as contiguous spheres or fiber-like representations alongside stacked genomic tracks showing gene annotations, proximity information from a selected viewpoint, and constraint information.
The project is no longer actively maintained or developed according to its repository notice, though the codebase remains available for reference and potential community use.
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