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Installation
User Guide
Models
ResolVI
DestVI
scVIVA
gimVI
Stereoscope
Tangram
Harreman
Background
Variational Inference
Differential Expression
Differential Abundance
Spatial Transcriptomics Methods
Use Cases
Saving and Loading Models
Training Configuration
Downstream Analysis
Tutorials
ResolVI to address noise and biases in spatial transcriptomics
Multi-resolution deconvolution of spatial transcriptomics with DestVI and Harreman
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
Metabolic zonation and crosstalk on the 10x Visium mouse colon dataset
API Reference
User API
scviva.model.SCVIVA
scviva.model.DestVI
scviva.model.ResolVI
scviva.model.GIMVI
scviva.external.RNAStereoscope
scviva.external.SpatialStereoscope
scviva.external.Tangram
scviva.tl.HarremanAnalysis
scviva.pl.harreman.local_correlation_plot
scviva.pl.harreman.average_local_correlation_plot
scviva.pl.harreman.module_score_correlation_plot
scviva.pl.harreman.plot_interacting_cell_scores
scviva.pl.harreman.plot_ct_interacting_cell_scores
scviva.pl.harreman.plot_interaction_module_correlation
scviva.pl.plot_cell_type_map
scviva.pl.scviva_de.plot_niche_de_decision_boundary
scviva.pl.scviva_de.plot_connectivity_distribution
scviva.settings
Developer API
scviva.model.base.SpatialBaseModel
scviva.model.base.SpatialNeighborhoodMixin
scviva.model.base.SpatialDeconvolutionMixin
scviva.model.base.SpatialPredictiveMixin
scviva.data.SpatialCoordsField
scviva.data.NeighborhoodGraphField
scviva.module.nicheVAE
scviva.module.JVAE
Developer Documentation
Contributing Code
Maintenance Guide
Frequently Asked Questions
Changelog
References
Discussion
GitHub
Model hub
Repository
Suggest edit
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.md
.pdf
Models
Models
#
ResolVI
DestVI
scVIVA
gimVI
Stereoscope
Tangram
Harreman