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HoloNet documentation

  • Installation
  • Tutorials
    • Analyzing and visualizing cell-cell communication events
    • Decoding the holograph of functional cell-cell communication events
  • API
    • HoloNet.preprocessing.load_brca_visium_10x
    • HoloNet.preprocessing.load_lr_df
    • HoloNet.preprocessing.get_expressed_lr_df
    • HoloNet.tools.elements_expr_df_calculate
    • HoloNet.tools.compute_ce_tensor
    • HoloNet.tools.filter_ce_tensor
    • HoloNet.tools.compute_ce_network_eigenvector_centrality
    • HoloNet.tools.compute_ce_network_degree_centrality
    • HoloNet.tools.cluster_lr_based_on_ce
    • HoloNet.tools.default_w_visium
    • HoloNet.predicting.get_continuous_cell_type_tensor
    • HoloNet.predicting.get_one_hot_cell_type_tensor
    • HoloNet.predicting.get_gene_expr
    • HoloNet.predicting.get_one_case_expr
    • HoloNet.predicting.adj_normalize
    • HoloNet.predicting.mgc_repeat_training
    • HoloNet.predicting.get_mgc_result
    • HoloNet.predicting.mgc_training_for_multiple_targets
    • HoloNet.predicting.get_mgc_result_for_multiple_targets
    • HoloNet.predicting.save_model_list
    • HoloNet.predicting.load_model_list
    • HoloNet.plotting.feature_plot
    • HoloNet.plotting.cell_type_level_network
    • HoloNet.plotting.plot_cell_type_proportion
    • HoloNet.plotting.ce_hotspot_plot
    • HoloNet.plotting.ce_cell_type_network_plot
    • HoloNet.plotting.lr_umap
    • HoloNet.plotting.lr_clustering_dendrogram
    • HoloNet.plotting.lr_cluster_ce_hotspot_plot
    • HoloNet.plotting.lr_rank_in_mgc
    • HoloNet.plotting.fce_cell_type_network_plot
    • HoloNet.plotting.delta_e_proportion
    • HoloNet.plotting.plot_mgc_result
    • HoloNet.plotting.find_genes_linked_to_ce
    • HoloNet.plotting.detect_pathway_related_genes
    • HoloNet.plotting.select_w
  • References
  • .rst

Tutorials

Tutorials#

Contents:

  • Analyzing and visualizing cell-cell communication events
  • Decoding the holograph of functional cell-cell communication events

The first tutorial mainly for analyzing and visualizing cell-cell communication events (CEs), corresponding to the first part of HoloNet:

_images/github_readme_figure03.png

The second tutorial mainly for decoding the holograph of functional cell-cell communication events (FCEs), corresponding to the second part of HoloNet:

_images/github_readme_figure04.png

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Analyzing and visualizing cell-cell communication events

By Li Haochen

© Copyright 2023, Li Haochen..