From f434292ea03db9da7cd7af9925e67acd445e9abe Mon Sep 17 00:00:00 2001 From: Benoit Putzeys Date: Wed, 22 May 2024 13:50:25 +0200 Subject: [PATCH] Add links to ReadTheDocs --- README.md | 3 ++- docs/intro.md | 6 +++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a867b8e1..90b57ed1 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,7 @@ pip install --upgrade --force-reinstall git+https://github.com/helicalAI/helical - [Universal Cell Embedding (UCE)](https://helical.readthedocs.io/en/latest/docs/UCE.html) ### DNA models: -- Coming soon +- [HyenaDNA](https://helical.readthedocs.io/en/latest/docs/hyena_dna.html) ## Demo & Use Cases @@ -73,6 +73,7 @@ A lot of our models have been published by talend authors developing these excit - [scGPT](https://github.com/bowang-lab/scGPT/) - [Geneformer](https://huggingface.co/ctheodoris/Geneformer) - [UCE](https://github.com/snap-stanford/UCE) +- [HyenaDNA](https://github.com/HazyResearch/hyena-dna) - [anndata](https://github.com/scverse/anndata) - [scanpy](https://github.com/scverse/scanpy) - [transformers](https://github.com/huggingface/transformers) diff --git a/docs/intro.md b/docs/intro.md index abb5d37a..8f97a891 100644 --- a/docs/intro.md +++ b/docs/intro.md @@ -38,11 +38,14 @@ 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` ### 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) - `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 +- [HyenaDNA](https://helical.readthedocs.io/en/latest/docs/hyena_dna.html) ## Stuck somewhere ? Other ideas ? We are eager to help you and interact with you. Reach out via support@helical-ai.com. @@ -66,6 +69,7 @@ A lot of our models have been published by talend authors developing these excit - [scGPT](https://github.com/bowang-lab/scGPT/) - [Geneformer](https://huggingface.co/ctheodoris/Geneformer) - [UCE](https://github.com/snap-stanford/UCE) +- [HyenaDNA](https://github.com/HazyResearch/hyena-dna) - [anndata](https://github.com/scverse/anndata) - [scanpy](https://github.com/scverse/scanpy) - [transformers](https://github.com/huggingface/transformers)