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.  

Integrate Hi-C with ChIP-seq.

Chromatin colors in 3D.

Identifying 3D genome hubs.

Code example of METALoci applied to H3K27ac for the Sox9 mouse locus during development (E13.5).  

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