Database of computational tools developed by members of the International Nucleome Consortium
This repository lists the computational tools developed by COST INC (http://inc-cost.eu/) members for data analysis and modeling in the context of 4D Genomics. To add your own tool to the database, fill the form https://forms.gle/DF62urBw5UAqgPkT9.
This summary table enumerates (non-exhaustively) the tasks performed by the different tools:
- Hi-C generation: functions to treat Hi-C raw data to generate Hi-C matrices or to import already processed Hi-C data
- Hi-C analysis: functions to analyze Hi-C data to infer/compare compartments, TADs, structural motifs, etc.
- Hi-C visualization: functions to visualize Hi-C data
- Image analysis: functions to treat and analyse images or movies from microscopy
- (Epi)genomic data analysis: functions to treat and analyse NGS (epi)genomic data
- Integrative 3D modeling: top-down reconstructions of 3D genome conformations from 4D genomics data
- Biophysical modeling: bottom-up biophysical/polymer/mechanistic models to predict chromatin organization based on mechanisms
- Statistical modeling: statistical/AI models to predict contacts, TAD boundaries, structural motifs, etc. based on genomics data
| Hi-C generation | Hi-C analysis | Hi-C visualization | Image analysis | (Epi)genomic Analysis | Integrative 3D modeling | Biophysical modeling | Statistical modeling | |
|---|---|---|---|---|---|---|---|---|
| 3DGenBench | X | X | X | |||||
| 3DPolyS-Epi | X | |||||||
| 3DPolyS-LE | X | |||||||
| 3DPredictor | X | |||||||
| Binless | X | X | ||||||
| Chrom3D | X | |||||||
| ChromFold | X | |||||||
| ChromHL | X | |||||||
| CharRM | X | X | ||||||
| CHESS | X | |||||||
| CHiCAGO | X | X | ||||||
| Chicdiff | X | X | ||||||
| C-InterSecture | X | X | ||||||
| essHi-C | X | X | ||||||
| FAN-C | X | X | X | |||||
| GENOVA | X | X | ||||||
| HIPPS | X | |||||||
| HiCBricks | X | X | X | |||||
| IC-Finder | X | |||||||
| IMGR | X | X | ||||||
| NRLcalc | X | X | ||||||
| NucTools | X | |||||||
| PHiC | X | |||||||
| ShRec3D | X | |||||||
| TADbit | X | X | X | X | ||||
| TADdyn | X | |||||||
| TADkit | X | |||||||
| TADpole | X | |||||||
| TFaffinity | X |