diff --git a/README.md b/README.md index c3e0bb3e..6ce166f8 100644 --- a/README.md +++ b/README.md @@ -5,13 +5,13 @@ # What is Helical ? -Helical provides a framework for and gathers state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities. +Helical provides a framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities. Helical simplifies the entire application lifecycle when building with bio foundation models. You will be able to: - Leverage the latest bio foundation models through our easy-to-use python package - Run example notebooks on key downstream tasks from examples -We will update this repo on a bi-weekly basis with new models, benchmarks, modalities and functions - so stay tuned. +We will update this repo on a regular basis with new models, benchmarks, modalities and functions - so stay tuned. Let’s build the most exciting AI-for-Bio community together! ## Installation @@ -26,24 +26,31 @@ To install the Helical package, you can run the command below: pip install --upgrade --force-reinstall git+https://github.com/helicalAI/helical.git ``` +## Installation +### RNA models: +- [Geneformer](https://helical.readthedocs.io/en/latest/docs/Geneformer.html) +- [scGPT](https://helical.readthedocs.io/en/latest/docs/scGPT.html) +- [Universal Cell Embedding (UCE)](https://helical.readthedocs.io/en/latest/docs/UCE.html) + +### DNA models: +- Coming soon + ## Demo & Use Cases To run examples, be sure to have installed the Helical package (see Installation) and that it is up-to-date. -You can look directly into the example folder above, look into our [documentation](https://helical.readthedocs.io/) for step-by-step guides or directly clone the repository using: +You can look directly into the example folder above and download the script of your choice, look into our [documentation](https://helical.readthedocs.io/) for step-by-step guides or directly clone the repository using: ``` git clone https://github.com/helicalAI/helical.git ``` -Within the `example` folder, open the notebook of your choice. We recommend starting with `Geneformer-vs-UCE.ipynb` +Within the `example` folder, open the notebook of your choice. We recommend starting with `Quick-Start_Tutorial.ipynb` -### RNA models: +### Current Examples: +- `Quick-Start_Tutorial.ipynb`: A tutorial to quickly get used to the helical package and enbironment. - `Geneformer-vs-UCE.ipynb`: Zero-Shot Reference Mapping with Geneformer & UCE and compare the outcomes. - Coming soon: new models such as scGPT, SCimilarity, scVI; benchmarking scripts; new use cases; others -### DNA models: -- Coming soon: new models such as Nucleotide Transformer; others - ## Stuck somewhere ? Other ideas ? We are eager to help you and interact with you. Reach out via support@helical-ai.com. You can also open github issues here. @@ -83,3 +90,6 @@ Please use this BibTeX to cite this repository in your publications: journal = {GitHub Repository}, howpublished = {\url{https://github.com/helicalAI/helical}}, } + + +