API Reference

Models

Core Models

model.SpatialVAE	Spatial Variational Autoencoder for spatial transcriptomics.
model.BaseSpatialModel	Base class for all spatial transcriptomics models.

External Models

external.AMICI	AMICI model for cell-cell interaction inference.
external.VIVS	VIVS model for identifying spatially variable genes.
external.Starfysh	Starfysh model for spatial deconvolution with histology.
external.Harreman	Harreman model for metabolic exchange inference.
external.Nolan	High-level interface to the NOLAN spatial niche model.
external.Lambda	Language-model based cell type annotation.
external.PPIInference	Static methods for prediction-powered inference.
external.SPARL	Interface to the SPARL representation learning model.
external.scVIVA	Wrapper for scvi-tools scVIVA model.
external.ResolVI	Wrapper for scvi-tools ResolVI model.
external.DestVI	Wrapper for scvi-tools DestVI model.

Modules

module.SpatialVAEModule	Spatial VAE module for gene expression modeling.
module.NicheModule	Module for niche-aware spatial analysis.
module.DeconvolutionModule	Module for spatial deconvolution.

Data

data.compute_spatial_neighbors	Compute spatial nearest neighbors.
data.compute_niche_composition	Compute neighborhood cell type composition.
data.synthetic_spatial	Generate synthetic spatial transcriptomics data.
data.synthetic_scrna	Generate synthetic single-cell RNA-seq data.

Neural Network Components

nn.SpatialEncoder	Encoder that incorporates spatial context.
nn.SpatialDecoder	Decoder that can incorporate spatial context for reconstruction.
nn.SpatialAttention	Spatial attention mechanism that weights neighbors by distance.
nn.NeighborAttention	Attention mechanism for aggregating neighbor information.

Training

train.SpatialTrainingPlan	Training plan with spatial-specific features.
train.NicheTrainingPlan	Training plan for niche-aware models.
train.DeconvolutionTrainingPlan	Training plan for spatial deconvolution models.

Utilities

utils.spatial_autocorrelation	Compute spatial autocorrelation for genes.
utils.plot_spatial	Plot cells in spatial coordinates.
utils.plot_proportions	Plot cell type proportions in spatial coordinates.