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spatialvi-tools

  • Installation
  • User Guide
    • Models
      • ResolVI
      • DestVI
      • scVIVA
    • Background
      • Variational Inference
      • Differential Expression
      • Spatial Transcriptomics Methods
    • Use Cases
      • Saving and Loading Models
      • Training Configuration
      • Downstream Analysis
  • API Reference
    • User API
      • spatialvi.model.SCVIVA
      • spatialvi.model.DestVI
      • spatialvi.model.ResolVI
      • spatialvi.model.GIMVI
      • spatialvi.external.RNAStereoscope
      • spatialvi.external.SpatialStereoscope
      • spatialvi.settings
    • Developer API
      • spatialvi.model.base.SpatialBaseModel
      • spatialvi.model.base.SpatialNeighborhoodMixin
      • spatialvi.model.base.SpatialDeconvolutionMixin
      • spatialvi.model.base.ResolVIPredictiveMixin
      • spatialvi.data.SpatialCoordsField
      • spatialvi.data.NeighborhoodGraphField
      • spatialvi.module.nicheVAE
      • spatialvi.module.JVAE
  • Developer Documentation
    • Contributing Code
    • Maintenance Guide
  • Tutorials
    • ResolVI to address noise and biases in spatial transcriptomics
    • Multi-resolution deconvolution of spatial transcriptomics
    • scVIVA for representing cells and their environment in spatial transcriptomics
    • Introduction to gimVI
    • Stereoscope applied to left ventricule data
    • Mapping human lymph node cell types to 10X Visium with Cell2location
    • Spatial mapping with Tangram
  • Frequently Asked Questions
  • References
  • Repository
  • Suggest edit
  • Open issue
  • .md

API Reference

API Reference#

Import spatialvi-tools as:

import spatialvi
  • User API
    • Models
    • External models
    • Settings
  • Developer API
    • Base classes
    • Data fields
    • Modules (neural networks)

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By Ori Kronfeld

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