kangk1204 / tadbit Goto Github PK

Current version: 0.1_alpha.801

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.

• TADbit documentation
• Summary of TADbit classes and functions

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

If you have any question remaining, we would be happy to answer informally:

• September 28th to October 2nd 2015: Chromosomal Conformation course at the CRG training programme Bracelona (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)