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  1. SpaBatch SpaBatch Public

    [Advanced Science 2025] SpaBatch: Deep learning-based cross-slice integration and 3D spatial domain identification in spatial transcriptomics

    Jupyter Notebook 14 2

  2. SpaCross SpaCross Public

    [Communications Biology 2025 (under Nature Portfolio)] SpaCross is a comprehensive analytical framework designed for spatial transcriptomics data, aiming to enhance the accuracy of spatial pattern …

    Jupyter Notebook 7

  3. SpaMask SpaMask Public

    [PLoS Computational Biology 2025] SpaMask: Dual Masking Graph Autoencoder with Contrastive Learning for Spatial Transcriptomics

    Jupyter Notebook 12

  4. SpaDAMA SpaDAMA Public

    [PLoS Computational Biology 2025] Domain-Adversarial Masked Autoencoder (SpaDAMA) for cell type deconvolution in spatial transcriptomics data

    Jupyter Notebook 10

  5. ZhicengShi/mclSTExp ZhicengShi/mclSTExp Public

    mclSTExp: Multimodal Contrastive Learning for Spatial Gene Expression Prediction Using Histology Images

    Jupyter Notebook 40

  6. scstGCN scstGCN Public

    [Briefings in Bioinformatics 2025] A GCN and pathology image large model-based method to predict single-cell resolution spatial gene expression by integrating multimodal information.

    Jupyter Notebook 26 1