Package: SpaCCI 1.0.5

Li-Ting Ku

SpaCCI: Spatially Aware Cell-Cell Interaction Analysis

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' <https://github.com/jinworks/CellChat>, 'CellPhoneDB' <https://www.cellphonedb.org/>, 'Cellinker' <https://www.rna-society.org/cellinker/>, 'ICELLNET' <https://github.com/soumelis-lab/ICELLNET>, and 'ConnectomeDB' <https://humanconnectome.org/software/connectomedb/> to identify ligand-receptor pairs, visualize interactions through heatmaps, chord diagrams, and infer interactions on different spatial scales.

Authors:Li-Ting Ku [aut, cre]

SpaCCI_1.0.5.tar.gz
SpaCCI_1.0.5.tar.gz(r-4.7-arm64)SpaCCI_1.0.5.tar.gz(r-4.7-x86_64)SpaCCI_1.0.5.tar.gz(r-4.6-arm64)SpaCCI_1.0.5.tar.gz(r-4.6-x86_64)
SpaCCI_1.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SpaCCI/json (API)

# Install 'SpaCCI' in R:

install.packages('SpaCCI', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

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
test_data - Test data for SpaCCI

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblas cpp

1.34 score 22 scripts 344 downloads 24 exports 148 dependencies

Last updated from:5d366077cd. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	245
linux-devel-x86_64	OK	286
source / vignettes	OK	238
linux-release-arm64	OK	243
linux-release-x86_64	OK	286
wasm-release	OK	209

Exports:Find_regional_IDs GetShuffledCT Global_Permutations Local_Regional_Permutations LR_database plot_localized plot_localized_Seurat plot_SpaCCI_chordDiagram plot_SpaCCI_heatmap plot_SpaCCI_local plot_SpaCCI_local_Strength plot_Strength_localized plot_Strength_Seurat possible_L_R_pairs_cellchat possible_L_R_pairs_Cellinker possible_L_R_pairs_cellphoneDB possible_L_R_pairs_connectome possible_L_R_pairs_ICELLNET random_region run_SpaCCI scPalette SpaCCI_global SpaCCI_local SpaCCI_region

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools circlize cli cluster codetools colorspace commonmark cowplot cpp11 crosstalk curl data.table deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggplot2 ggrepel ggridges GlobalOptions globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix matrixStats memoise mime miniUI nlme nnls openssl otel parallelly patchwork pbapply pheatmap pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S7 sass scales scattermore sctransform Seurat SeuratObject shape shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

Citation

Readme and manuals

Help Manual

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

Package: SpaCCI 1.0.5

SpaCCI: Spatially Aware Cell-Cell Interaction Analysis

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)