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MetaChat 0.0.6 documentation
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Contents:

  • Installation
  • Basic tutorials
    • Identifying Anatomical Features
      • Identifying Long-Range Channels (LRCs)
      • Annotating barrier condition
    • Estimating Spatial Metabolomics from Spatial Transcriptomics
      • using scFEA
      • using COMPASS
      • using MEBOCOST
    • Tip for Analyzing Multiple Slides or Biological Replicates
    • Guideline for Function and Visualization
  • Real dataset tutorials
    • Spatial Multi-Omics Data from Mouse Brain with Parkinson’s Disease
      • MetaChat analysis
      • Comparative analysis
      • Downstream analysis
    • Spatial Multi-Omics Data from Human Gastric Cancer
      • MetaChat analysis
      • Downstream analysis
    • Visium HD Dataset from Mouse Small Intestine
      • MetaChat analysis
      • Downstream analysis
    • 3D Transcriptomics Dataset from Whole Mouse Brain
      • MetaChat analysis and Downstream analysis
  • API
    • metachat.pp.MetaChatDB
    • metachat.pp.generate_adata_met_compass
    • metachat.pp.generate_adata_met_scFEA
    • metachat.pp.generate_adata_met_mebocost
    • metachat.pp.global_intensity_scaling
    • metachat.pp.load_barrier_segments
    • metachat.pp.LRC_unfiltered
    • metachat.pp.LRC_cluster
    • metachat.pp.LRC_filtered
    • metachat.pp.compute_costDistance
    • metachat.tl.metabolic_communication
    • metachat.tl.summary_communication
    • metachat.tl.communication_flow
    • metachat.tl.communication_group
    • metachat.tl.communication_group_spatial
    • metachat.tl.summary_pathway
    • metachat.tl.communication_responseGenes
    • metachat.tl.communication_responseGenes_cluster
    • metachat.tl.communication_responseGenes_keggEnrich
    • metachat.tl.compute_direction_histogram_per_pair
    • metachat.pl.plot_communication_flow
    • metachat.pl.plot_group_communication_chord
    • metachat.pl.plot_group_communication_heatmap
    • metachat.pl.plot_group_communication_compare_hierarchy_diagram
    • metachat.pl.plot_MSpair_contribute_group
    • metachat.pl.plot_summary_pathway
    • metachat.pl.plot_metapathway_pair_contribution_bubbleplot
    • metachat.pl.plot_communication_responseGenes
    • metachat.pl.plot_communication_responseGenes_keggEnrich
    • metachat.pl.plot_DEG_volcano
    • metachat.pl.plot_3d_feature
    • metachat.pl.plot_3d_LRC_with_two_slices
    • metachat.pl.plot_dis_thr
    • metachat.pl.plot_LRC_markers
    • metachat.pl.plot_spot_distance
    • metachat.pl.plot_graph_connectivity
    • metachat.pl.plot_direction_similarity
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3D Transcriptomics Dataset from Whole Mouse Brain

  • MetaChat analysis and Downstream analysis
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MetaChat and downstream analysis on 3D transcriptomics from whole mouse brain
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