Package: SpaCCI 1.0.2

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' <http://www.cellchat.org/>, '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_1.0.2.tar.gz
SpaCCI_1.0.2.tar.gz(r-4.5-noble)SpaCCI_1.0.2.tar.gz(r-4.4-noble)
SpaCCI_1.0.2.tgz(r-4.4-emscripten)
SpaCCI.pdf |SpaCCI.html✨
SpaCCI/json (API)

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

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

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

1.53 score 17 scripts 199 downloads 21 exports 151 dependencies

Last updated 2 days agofrom:a576b905fd. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-linux-x86_64OKOct 25 2024

Exports:Find_regional_IDsGetShuffledCTGlobal_PermutationsLocal_Regional_PermutationsLR_databaseplot_localizedplot_localized_Seuratplot_SpaCCI_chordDiagramplot_SpaCCI_heatmapplot_SpaCCI_localpossible_L_R_pairs_cellchatpossible_L_R_pairs_Cellinkerpossible_L_R_pairs_cellphoneDBpossible_L_R_pairs_connectomepossible_L_R_pairs_ICELLNETrandom_regionrun_SpaCCIscPaletteSpaCCI_globalSpaCCI_localSpaCCI_region

Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscirclizecliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmennlsopensslparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshapeshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Find the spatial neighborhood Spot IDsFind_regional_IDs
Perform a Deranged Shuffle of Cell TypesGetShuffledCT
Perform Global PermutationsGlobal_Permutations
Perform Local and Regional PermutationsLocal_Regional_Permutations
Identify Possible Ligand-Receptor Pairs for Cell-Cell CommunicationLR_database
Plot Localized Hotspot Patternplot_localized
Plot Localized Hotspot Pattern on Seurat Objectplot_localized_Seurat
Plot SpaCCI Results on Chord Diagramplot_SpaCCI_chordDiagram
Plot SpaCCI Results on the heatmap Visualize inferred significant cell-cell interactions using a heatmapplot_SpaCCI_heatmap
Plot SpaCCI Localized Interaction Resultsplot_SpaCCI_local
CellChat Database: Identify Possible Ligand-Receptor Pairs for Cell-Cell Communicationpossible_L_R_pairs_cellchat
Identify Possible Ligand-Receptor Pairs for Cell-Cell Communicationpossible_L_R_pairs_Cellinker
Identify Possible Ligand-Receptor Pairs for Cell-Cell Communicationpossible_L_R_pairs_cellphoneDB
Identify Possible Ligand-Receptor Pairs for Cell-Cell Communicationpossible_L_R_pairs_connectome
Identify Possible Ligand-Receptor Pairs for Cell-Cell Communicationpossible_L_R_pairs_ICELLNET
Select Closest Spatial IDs to a Center Point: this is used for permutationrandom_region
result_global data for SpaCCIresult_global
result_local data for SpaCCIresult_local
Run SpaCCI Analysisrun_SpaCCI
Generate a Color PalettescPalette
Infer Cell-Cell Interactions on a Global ScaleSpaCCI_global
Infer Cell-Cell Interactions on a Local ScaleSpaCCI_local
Infer Cell-Cell Interactions in a Specified RegionSpaCCI_region
Test data for SpaCCItest_data