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SpaCCI (version 1.0.4)

Spatially Aware Cell-Cell Interaction Analysis

Description

Provides tools for analyzing spatial cell-cell interactions based on ligand-receptor pairs, including functions for local, regional, and global analysis using spatial transcriptomics data. Integrates with databases like 'CellChat' , 'CellPhoneDB' , 'Cellinker' , 'ICELLNET' , and 'ConnectomeDB' to identify ligand-receptor pairs, visualize interactions through heatmaps, chord diagrams, and infer interactions on different spatial scales.

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Version

Install

install.packages('SpaCCI')

Monthly Downloads

138

Version

1.0.4

License

GPL (>= 2)

Maintainer

Li-Ting Ku

Last Published

May 12th, 2025

Functions in SpaCCI (1.0.4)

Global_Permutations

Perform Global Permutations
GetShuffledCT

Perform a Deranged Shuffle of Cell Types
possible_L_R_pairs_ICELLNET

Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
plot_localized

Plot Localized Hotspot Pattern
plot_Strength_localized

Plot Localized Hotspot Strength Pattern
possible_L_R_pairs_cellchat

CellChat Database: Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
plot_localized_Seurat

Plot Localized Hotspot Pattern on Seurat Object
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_Strength_Seurat

Plot Localized Hotspot Strength Pattern on Seurat Object
plot_SpaCCI_local_Strength

Plot SpaCCI Localized Interaction Strength Results
possible_L_R_pairs_Cellinker

Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
run_SpaCCI

Run SpaCCI Analysis
result_local

result_local data and spatial coordinates for SpaCCI Local Regional Data
result_regional

result_regional data for SpaCCI
random_region

Select Closest Spatial IDs to a Center Point: this is used for permutation
scPalette

Generate a Color Palette
self_identified_LR

Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
test_data

Test data for SpaCCI
result_local_spatial_coords_df

Local Spatial Coordinates Data Frame
result_global

result_global data for SpaCCI
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
LR_database

Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
SpaCCI_local

Infer Cell-Cell Interactions on a Local Scale
Local_Regional_Permutations

Perform Local and Regional Permutations
SpaCCI_global

Infer Cell-Cell Interactions on a Global Scale
SpaCCI_region

Infer Cell-Cell Interactions in a Specified Region
plot_SpaCCI_chordDiagram

Plot SpaCCI Results on Chord Diagram
DB_dataframe

Test data for SpaCCI
Find_regional_IDs

Find the spatial neighborhood Spot IDs