| license: gpl-3.0 | |
| library_name: pytorch | |
| tags: | |
| - nanopore | |
| - dna-modification | |
| - methylation | |
| - raw-signal | |
| # RawMod | |
| Pretrained models for **RawMod: Modification-Agnostic Detection of DNA Base | |
| Modifications from Nanopore Signal Pileups**. | |
| RawMod detects modified DNA bases directly from raw nanopore signals. One model | |
| detects 5mC, 5hmC, 6mA, 4mC and 5hmU, and it needs no unmodified control. | |
| Code, installation, usage and full documentation: | |
| **https://github.com/STORMgroup/RawMod** | |
| ## Files | |
| | Path | Use | | |
| |---|---| | |
| | `rawmod.pt` | The released model. Use this one to score new data. | | |
| | `region_holdout/` | Models trained without one region of every genome. Used for the accuracy numbers of the paper. `loco_<mod>.pt` also withholds one modification type. `seeds/` holds two more training seeds. | | |
| | `leaveout/` | Models trained without one organism or library. Used for the paper's supplementary leave-out benchmark. | | |
| All files share one architecture (230,697 parameters). They are PyTorch state | |
| dictionaries for the code in the GitHub repository. `SHA256SUMS` lists the | |
| checksums of every file. | |
| ## Download | |
| ```bash | |
| hf download STORMResearch/RawMod --local-dir checkpoints | |
| ``` | |
| ## Citation | |
| The RawMod paper is under review. Until it is published, please cite the | |
| GitHub repository: https://github.com/STORMgroup/RawMod. | |