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  • Installation
  • API
    • stlearn.read_10x
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    • stlearn.read_slide_seq
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    • stlearn.read_xenium
    • stlearn.create_stlearn
    • stlearn.convert_scanpy
    • stlearn.add.image
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    • stlearn.pp.filter_genes
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    • stlearn.em.run_pca
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    • stlearn.spatial.clustering.localization
    • stlearn.spatial.trajectory.pseudotime
    • stlearn.spatial.trajectory.pseudotimespace_global
    • stlearn.spatial.trajectory.pseudotimespace_local
    • stlearn.spatial.trajectory.compare_transitions
    • stlearn.spatial.trajectory.detect_transition_markers_clades
    • stlearn.spatial.trajectory.detect_transition_markers_branches
    • stlearn.spatial.trajectory.set_root
    • stlearn.spatial.morphology.adjust
    • stlearn.spatial.sme.sme_impute0
    • stlearn.spatial.sme.pseudo_spot
    • stlearn.spatial.sme.sme_normalize
    • stlearn.tl.clustering.kmeans
    • stlearn.tl.clustering.leiden
    • stlearn.tl.cci.load_lrs
    • stlearn.tl.cci.grid
    • stlearn.tl.cci.run
    • stlearn.tl.cci.adj_pvals
    • stlearn.tl.cci.run_lr_go
    • stlearn.tl.cci.run_cci
    • stlearn.pl.qc_plot
    • stlearn.pl.gene_plot
    • stlearn.pl.gene_plot_interactive
    • stlearn.pl.cluster_plot
    • stlearn.pl.cluster_plot_interactive
    • stlearn.pl.subcluster_plot
    • stlearn.pl.non_spatial_plot
    • stlearn.pl.deconvolution_plot
    • stlearn.pl.plot_mask
    • stlearn.pl.lr_summary
    • stlearn.pl.lr_diagnostics
    • stlearn.pl.lr_n_spots
    • stlearn.pl.lr_go
    • stlearn.pl.lr_result_plot
    • stlearn.pl.lr_plot
    • stlearn.pl.cci_check
    • stlearn.pl.ccinet_plot
    • stlearn.pl.lr_chord_plot
    • stlearn.pl.lr_cci_map
    • stlearn.pl.cci_map
    • stlearn.pl.lr_plot_interactive
    • stlearn.pl.spatialcci_plot_interactive
    • stlearn.pl.trajectory.pseudotime_plot
    • stlearn.pl.trajectory.local_plot
    • stlearn.pl.trajectory.tree_plot
    • stlearn.pl.trajectory.transition_markers_plot
    • stlearn.pl.trajectory.de_transition_plot
    • stlearn.datasets.visium_sge
    • stlearn.datasets.xenium_sge
  • Tutorials
    • Cell-Cell Interaction Analysis
    • Cell-Cell Interaction Analysis with Xenium Data
    • Pseudotime Spatial Trajectory Inference
    • Pseudotime Spatial Trajectory Inference with Xenium Data
    • stSME Clustering
    • stSME Comparison
    • Normal
    • stSME
    • Marker gene for CA3
    • Marker gene for DG
    • Core Plotting Functions
    • Integrating Multiple Datasets
    • Working with scanpy Package
  • Release Notes
  • Credits
  • References
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TutorialsΒΆ

Main features:

Cell-Cell Interaction Analysis
Cell-Cell Interaction Analysis with Xenium Data
Pseudotime Spatial Trajectory Inference
Pseudotime Spatial Trajectory Inference with Xenium Data
stSME Clustering
stSME Comparison

Visualisation and additional functionalities:

Core Plotting Functions
Integrating Multiple Datasets

Integration with other spatial tools:

Working with scanpy Package
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Cell-Cell Interaction Analysis
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stlearn.datasets.xenium_sge
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