Repositories list

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

  Public
  MIT License

  •42•409•3•1•Updated Jan 21, 2026Jan 21, 2026

• dance

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

  pythondata-sciencebenchmark+ 11machine-learningbioinformaticsdeep-learningcomputational-biologydancesingle-cellmultimodality+ 4

  Python

  •

  BSD 2-Clause "Simplified" License

  •36•384•27•7•Updated Jan 19, 2026Jan 19, 2026

• scLinguist

  Public
  The official repo for scLinguist

  Python

  •

  MIT License

  •0•7•1•1•Updated Oct 11, 2025Oct 11, 2025

• awesome-genetic-perturbation-papers

  Public
  0•5•0•0•Updated Aug 20, 2025Aug 20, 2025

• Mem-GAN

  Public

  OmicsML/Mem-GAN’s past year of commit activity
  A generative model for pseudo membrane generation of single-cell imaging in fluorescent microscopy

  Python

  •

  MIT License

  •0•8•0•0•Updated Jun 28, 2025Jun 28, 2025

• awesome-AI_Scientist-agents-biology-papers

  Public

  OmicsML/awesome-AI_Scientist-agents-biology-papers’s past year of commit activity
  3•52•6•0•Updated Apr 20, 2025Apr 20, 2025

• awesome-multimodal-multiomic-multiscale-papers

  Public

  OmicsML/awesome-multimodal-multiomic-multiscale-papers’s past year of commit activity
  0•2•0•0•Updated Apr 20, 2025Apr 20, 2025

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

  Public

  OmicsML/awesome-deep-learning-single-cell-papers’s past year of commit activity
  Apache License 2.0

  •112•839•13•4•Updated Apr 20, 2025Apr 20, 2025

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

  Public
  0•1•0•0•Updated Apr 20, 2025Apr 20, 2025

• awesome-foundation-model-DNA-papers

  Public
  0•3•0•0•Updated Jan 13, 2025Jan 13, 2025

• test.io

  Public
  test

  0•0•0•0•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

  •1•43•2•0•Updated Sep 15, 2024Sep 15, 2024

• scDiff

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

  Python

  •

  MIT License

  •4•32•3•0•Updated Aug 13, 2024Aug 13, 2024

• focus

  Public
  Python

  •0•5•2•0•Updated Aug 3, 2024Aug 3, 2024

• scLLMBench

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

  MIT License

  •1•0•0•0•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

  •13•101•10•0•Updated Mar 28, 2024Mar 28, 2024

• awesome-molecule-protein-pretrain-papers

  Public
  3•46•0•0•Updated Mar 11, 2024Mar 11, 2024

• scMoMem

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

  •0•0•0•0•Updated Feb 9, 2024Feb 9, 2024

• scMoFormer

  Public
  Single-Cell Multimodal Prediction via Transformer

  Python

  •

  MIT License

  •3•28•2•0•Updated Feb 7, 2024Feb 7, 2024

• dance-tutorials

  Public
  Jupyter Notebook

  •

  MIT License

  •0•5•1•0•Updated Nov 13, 2023Nov 13, 2023

• awesome-bio-chatgpt

  Public
  MIT License

  •0•22•0•0•Updated Apr 27, 2023Apr 27, 2023