Repositories list

• awesome-foundation-model-single-cell-papers

  Public
  surveysingle-cell-multiomicslarge-language-models+ 3

  surveysingle-cell-multiomicslarge-language-modelsai-virtual-cellsingle-cell-foundation-modelbiological-foundation-model

  MIT License

  •5454 forks•485485 stars•33 issues•22 pull requests•Updated Jun 24, 2026Jun 24, 2026

• dance

  Public
  DANCE: a deep learning library and benchmark platform for single-cell analysis

  pythondata-sciencebenchmark+ 11

  pythondata-sciencebenchmarkmachine-learningbioinformaticsdeep-learningcomputational-biologydancesingle-cellmultimodality+ 4

  Python

  •

  BSD 2-Clause "Simplified" License

  •3737 forks•389389 stars•2626 issues•88 pull requests•Updated Apr 27, 2026Apr 27, 2026

• scLinguist

  Public
  The official repo for scLinguist

  Python

  •

  MIT License

  •00 forks•99 stars•22 issues•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• awesome-genetic-perturbation-papers

  Public
  00 forks•66 stars•00 issues•00 pull requests•Updated Aug 20, 2025Aug 20, 2025

• Mem-GAN

  Public
  A generative model for pseudo membrane generation of single-cell imaging in fluorescent microscopy

  Python

  •

  MIT License

  •00 forks•88 stars•00 issues•00 pull requests•Updated Jun 28, 2025Jun 28, 2025

• awesome-AI_Scientist-agents-biology-papers

  Public
  55 forks•5757 stars•77 issues•22 pull requests•Updated Apr 20, 2025Apr 20, 2025

• awesome-multimodal-multiomic-multiscale-papers

  Public
  00 forks•22 stars•00 issues•00 pull requests•Updated Apr 20, 2025Apr 20, 2025

• awesome-deep-learning-single-cell-papers

  Public
  Apache License 2.0

  •115115 forks•861861 stars•1313 issues•55 pull requests•Updated Apr 20, 2025Apr 20, 2025

• awesome-sythetic-single-cell-data-papers

  Public
  00 forks•11 star•00 issues•00 pull requests•Updated Apr 20, 2025Apr 20, 2025

• awesome-foundation-model-DNA-papers

  Public
  00 forks•33 stars•00 issues•00 pull requests•Updated Jan 13, 2025Jan 13, 2025

• test.io

  Public
  test

  00 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2024Sep 22, 2024

• SpatialCTD

  Public
  A large scale atlas coming with Graph Neural Network solution for spatial cell type deconvolution

  Jupyter Notebook

  •

  MIT License

  •11 fork•4343 stars•22 issues•00 pull requests•Updated Sep 15, 2024Sep 15, 2024

• scDiff

  Public
  scDiff: A General Single-Cell Analysis Framework via Conditional Diffusion Generative Models

  Python

  •

  MIT License

  •44 forks•3434 stars•33 issues•00 pull requests•Updated Aug 13, 2024Aug 13, 2024

• focus

  Public
  Python

  •00 forks•66 stars•22 issues•00 pull requests•Updated Aug 3, 2024Aug 3, 2024

• scLLMBench

  Public
  scLLMBench: A fexible framework for accelerating single-cell foundation model benchmarking

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 8, 2024Apr 8, 2024

• CellPLM

  Public
  Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •1515 forks•104104 stars•1010 issues•00 pull requests•Updated Mar 28, 2024Mar 28, 2024

• awesome-molecule-protein-pretrain-papers

  Public
  55 forks•4747 stars•00 issues•11 pull request•Updated Mar 11, 2024Mar 11, 2024

• scMoMem

  Public
  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 9, 2024Feb 9, 2024

• scMoFormer

  Public
  Single-Cell Multimodal Prediction via Transformer

  Python

  •

  MIT License

  •44 forks•2727 stars•22 issues•00 pull requests•Updated Feb 7, 2024Feb 7, 2024

• dance-tutorials

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•55 stars•11 issue•00 pull requests•Updated Nov 13, 2023Nov 13, 2023

• awesome-bio-chatgpt

  Public
  MIT License

  •00 forks•2222 stars•00 issues•00 pull requests•Updated Apr 27, 2023Apr 27, 2023