iosonoirene/TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Current version: v0.2.0.33

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify adn compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models.

Hi-C experiments generate genomic interaction between loci located in the same or in different chromosomes. TADbit is built around the concept of a chromosome, and uses it as a central item to store and compare different Hi-C experiments. The library has been designed to be used by researchers with no expertise in computer science. All-in-one scripts provided in TADbit allow to run the full analysis using one single command line; advanced users may produce their own programs using TADbit as a complementary library.

Documentation

• TADbit documentation
• Summary of TADbit classes and functions

Citation

Serra, F., Baù, D., Filion, G., & Marti-Renom, M. A. (2016). Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling. bioRxiv. doi:10.1101/036764

Feedback

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TADbit training

Next editions

• April 3rd to April 7th 2016: Chromosomal Conformation course at the CRG training programme Barcelona (Spain)
• April 10th to April 11th 2016: MuG workshop: Multi-scale study of 3D Chromatin structure at the European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, (United Kingdom)

Past editions

• October 10th to October 14th 2016: 3DAROC16 3C-based data analysis and 3D reconstruction of chromatin folding at the GTPB training programme Oeiras (Portugal)
• September 28th to October 2nd 2015: Chromosomal Conformation course at the CRG training programme Barcelona (Spain)
• November 25th to November 28th 2014: CSDM 2014 at the GTPB training programme Oeiras (Portugal)
• September 6th 2014: TADbit: Automated Analysis and Three-Dimensional Modeling of Genomic Domains at ECCB14 Strasbourg (France)
• November 27th to November 29th 2013: CSDM 2013 at the GTPB training programme Oeiras (Portugal)