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STEP documentation
STEP documentation
  • Installation
  • Usage
    • EntryPoints
    • Results Storage
  • Tutorials
    • Spatial domain identification on 10x Visium DLFPC data
    • Performing integrative analysis on scRNA-seq data and 10x Visium data of Human Lymph Node with STEP
    • Reveal multiple level of biological heterogeneities in Mouse Hypothalamus by MERFISH-seq
    • Integrate Human Immune Cell datasets with STEP and generate batch-corrected embeddings and gene expressions.
    • Visium HD Human Colorectal Cancer (16 um) cell type clustering & spatial domain identification
    • Visium HD Mouse Small Intestine (8 um and 16 um) cell type clustering & spatial domain identification
  • API Reference
    • step
      • step.functionality
        • step.functionality.comps
          • step.functionality.comps.model_ops
          • step.functionality.comps.trainer
        • step.functionality.base
        • step.functionality.cross_funcmodel
        • step.functionality.sc_funcmodel
        • step.functionality.st_funcmodel
      • step.manager
        • step.manager.save
      • step.models
        • step.models.clust
        • step.models.deconv
        • step.models.distributions
        • step.models.extension
        • step.models.knn_map
        • step.models.nnls
        • step.models.transcriptformer
      • step.modules
        • step.modules.decoder
        • step.modules.gnn
        • step.modules.transformer
      • step.utils
        • step.utils.synthetics
          • step.utils.synthetics.pseudo_st
        • step.utils.dataset
        • step.utils.gbolt
        • step.utils.metrics
        • step.utils.misc
        • step.utils.plotting
      • step.integration
      • step.scmodel
      • step.stmodel
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