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Installation
User guide
Tutorials
Hotspot tutorials
Spatial data from Slide-seq
Transcriptional Patterns in CD4 T Cells
Harreman tutorials
Metabolic zonation on the Slide-TCR-seq human lung RCC dataset
Metabolic crosstalk on the Slide-TCR-seq human lung RCC dataset
Metabolic zonation on the 10x Visium mouse colon dataset
Metabolic crosstalk on the 10x Visium mouse colon dataset
API
harreman.datasets.load_visium_mouse_colon_dataset
harreman.datasets.load_slide_seq_human_lung_dataset
harreman.hotspot.load_metabolic_genes
harreman.hotspot.compute_local_autocorrelation
harreman.hotspot.compute_local_correlation
harreman.hotspot.create_modules
harreman.hotspot.calculate_module_scores
harreman.hotspot.compute_top_scoring_modules
harreman.hotspot.calculate_super_module_scores
harreman.preprocessing.extract_interaction_db
harreman.preprocessing.setup_deconv_adata
harreman.tools.compute_knn_graph
harreman.tools.apply_gene_filtering
harreman.tools.compute_gene_pairs
harreman.tools.compute_cell_communication
harreman.tools.compute_ct_cell_communication
harreman.tools.select_significant_interactions
harreman.tools.compute_interacting_cell_scores
harreman.tools.compute_ct_interacting_cell_scores
harreman.tools.compute_interaction_module_correlation
harreman.plots.local_correlation_plot
harreman.plots.average_local_correlation_plot
harreman.plots.module_score_correlation_plot
harreman.plots.plot_interacting_cell_scores
harreman.plots.plot_ct_interacting_cell_scores
harreman.read_h5ad
harreman.write_h5ad
Release notes
GitHub
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