Tools for modeling and analyzing 3D genomes.

Building 3D genomes.

TADbit is a computational package that uses 3C-based data to detect, model and analyze the structure of genomes and genomic domains.

Simulating over time 3D genomes.

TADdyn is a Python library that allows to model and explore single or time-series 3C-based data.
 

Finding hierarchical TADs in 3D genomes.

TADpole is a computational tool designed to identify and analyze the entire hierarchy of topologically associated domains (TADs) in intra-chromosomal interaction matrices.

Visualizing 3D genomes.

TADkit is a visualizer for 3D genomic data that helps researchers to easy annotate 3D models generated by TADbit.  

Normalize Hi-C data in non-binned datasets.

Resolution-independent normalization of Hi-C data.

Comparing Hi-C datasets.

CHESS is a tool for the comparison and automatic feature extraction for chromatin contact data.  

Link to datasets for developers of methods of 3D Genome building and a list of other methods for 3D genomics.