ColabRNA

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Making RNA-based models accessible to all.

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# ColabRNA

Inspired by [ColabFold](https://github.com/sokrypton/ColabFold), a repository aiming to make RNA-based models accessible to all.

![](https://raw.githubusercontent.com/MiqG/ColabRNA/main/profiles.png)

## Model notebooks
### Splicing
- [SpliceAI](https://colab.research.google.com/github/MiqG/ColabSplice/blob/main/notebooks/SpliceAI.ipynb)
- [Pangolin](https://colab.research.google.com/github/MiqG/ColabSplice/blob/main/notebooks/Pangolin.ipynb)
- [SpliceTransformer](https://colab.research.google.com/github/MiqG/ColabSplice/blob/main/notebooks/SpliceTransformer.ipynb)

### Transcriptomics
- [Borzoi](https://colab.research.google.com/github/MiqG/ColabSplice/blob/main/notebooks/Borzoi.ipynb)

### Nucleotide probability
- [RiNALMo](): TODO
- [RNABERT](): TODO

## References
- **SpliceAI**
    - repository: https://github.com/Illumina/SpliceAI
    - paper: https://doi.org/10.1016/j.cell.2018.12.015
- **Pangolin**
    - repository: https://github.com/tkzeng/Pangolin
    - paper: https://doi.org/10.1186/s13059-022-02664-4
- **SpliceTransformer**
    - repository: https://github.com/ShenLab-Genomics/SpliceTransformer
    - paper: https://doi.org/10.1038/s41467-024-53088-6
- **Borzoi**
    - original repository: https://github.com/calico/borzoi
    - original paper: https://doi.org/10.1038/s41588-024-02053-6
    - pytorch version:
        - repository: https://github.com/johahi/borzoi-pytorch
        - paper: https://doi.org/10.1101/2024.12.18.629121
- **RiNALMo**:
    - repository: https://github.com/lbcb-sci/RiNALMo
    - paper: https://arxiv.org/abs/2403.00043
- **RNABERT**:
    - repository: https://github.com/mana438/RNABERT
    - paper: https://doi.org/10.1093/nargab/lqac012

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