Spatially Aware Cell-Cell Interaction Analysis

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Documentation for package ‘SpaCCI’ version 1.0.3

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Find_regional_IDs Find the spatial neighborhood Spot IDs
GetShuffledCT Perform a Deranged Shuffle of Cell Types
Global_Permutations Perform Global Permutations
Local_Regional_Permutations Perform Local and Regional Permutations
LR_database Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
plot_localized Plot Localized Hotspot Pattern
plot_localized_Seurat Plot Localized Hotspot Pattern on Seurat Object
plot_SpaCCI_chordDiagram Plot SpaCCI Results on Chord Diagram
plot_SpaCCI_heatmap Plot SpaCCI Results on the heatmap Visualize inferred significant cell-cell interactions using a heatmap
plot_SpaCCI_local Plot SpaCCI Localized Interaction Results
plot_SpaCCI_local_Strength Plot SpaCCI Localized Interaction Strength Results
plot_Strength_localized Plot Localized Hotspot Strength Pattern
plot_Strength_Seurat Plot Localized Hotspot Strength Pattern on Seurat Object
possible_L_R_pairs_cellchat CellChat Database: Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
possible_L_R_pairs_Cellinker Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
possible_L_R_pairs_cellphoneDB Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
possible_L_R_pairs_connectome Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
possible_L_R_pairs_ICELLNET Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
random_region Select Closest Spatial IDs to a Center Point: this is used for permutation
result_global result_global data for SpaCCI
result_local result_local data and spatial coordinates for SpaCCI Local Regional Data
result_local_spatial_coords_df Local Spatial Coordinates Data Frame
result_regional result_regional data for SpaCCI
run_SpaCCI Run SpaCCI Analysis
scPalette Generate a Color Palette
SpaCCI_global Infer Cell-Cell Interactions on a Global Scale
SpaCCI_local Infer Cell-Cell Interactions on a Local Scale
SpaCCI_region Infer Cell-Cell Interactions in a Specified Region
test_data Test data for SpaCCI