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LYNX
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  • Overview
  • Installation
  • Installing into an existing interpreter
  • Using the tutorials in Jupyter
  • Tutorials
    • Liver β€” Xenium transcriptomics + DESI metabolomics
    • Breast β€” Xenium transcriptomics + H&E histology
    • Thymus β€” spatial RNA + protein (CITE-seq)
  • API reference
    • Model
      • lynx.model.HeteroAttnVGAE
      • lynx.dataset.HeteroDataset
      • lynx.dataset.XeniumDataset
      • lynx.config.set_model_configs
      • lynx.config.set_train_configs
    • Trajectory
      • lynx.trajectory.get_curve
      • lynx.trajectory.get_tree
      • lynx.trajectory.compute_pseudotime
      • lynx.trajectory.sort_nodes
      • lynx.trajectory.prune_tree
      • lynx.trajectory.get_cell_projections
    • Zonation & utilities
      • lynx.utils.get_zonations
      • lynx.utils.get_zonation_features
      • lynx.utils.get_binned_expr
      • lynx.utils.get_celltype_dynamics
      • lynx.utils.get_cluster_dynamics
      • lynx.utils.sort_fitted_expr
    • Plotting
      • lynx.plot.disp_trajectory
      • lynx.plot.disp_kde_scatter
      • lynx.plot.disp_heatmap
      • lynx.plot.disp_stacked_dynamics
      • lynx.plot.disp_spatial_latents
      • lynx.plot.disp_joint_logfc
      • lynx.plot.summarize_cell_interaction
      • lynx.plot.netVisual_circle
    • Association tests
      • lynx.test_assoc.test_cci
      • lynx.test_assoc.test_trajectory
      • lynx.test_assoc.get_test_associations
    • IO
      • lynx.io.load_xenium
      • lynx.io.filter_cells
      • lynx.io.load_ab_stain
      • lynx.io.load_spatial_metadata
      • lynx.io.load_annot_tiffs
      • lynx.io.save_annot_tifs
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ModelΒΆ

The heterogeneous attention VGAE and its configuration / dataset helpers.

model.HeteroAttnVGAE

Learning latent manifold w/ Conditional VGAE on hetero-graph Generative path: DESI (u) -> Latent (z) -> Xenium (x)

dataset.HeteroDataset

Load paired multi-modal ST data w/ hybrid resolutions into a hetero-graph

dataset.XeniumDataset

Load Xenium ST graph w/ auxiliary DESI modality

config.set_model_configs

config.set_train_configs

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