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Tools for modeling and analyzing 3D genomes. |
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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). |
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Link to datasets for developers of methods of 3D Genome building and a list of other methods for 3D genomics. |