We started a project on benchmarking of software for 3D chromatin organisation – please see here how you can contribute: https://inc-cost.eu/benchmarking

The database below lists software developed by INC members for nucleome data analysis and modeling.

The interactive table below classifies (non-exhaustively) the tools by the following tasks:

• Hi-C generation: from raw Hi-C data to Hi-C matrices, etc
• Hi-C analysis: infer/compare compartments, TADs, structural motifs, etc, from Hi-C data.
• Hi-C visualization: functions to visualize Hi-C data
• Image analysis: functions to process and analyse images or movies from microscopy
• Integrative modeling: reconstructions of 3D genome conformations from 4D genomics data
• Biophysical modeling: bottom-up thermodynamic/mechanistic models to predict chromatin organization
• Statistical modeling: statistical models to predict contacts, TAD boundaries, structural motifs, etc.
• Nucleosome analysis: Inferring nucleosome landscapes from sequencing data