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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
  • .md

Tutorials

Tutorials#

Get started with Harreman by following our 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

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Hotspot tutorials

By Oier Etxezarreta Arrastoa

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