Package: SpaCCI 1.0.3

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:
SpaCCI_1.0.3.tar.gz
SpaCCI_1.0.3.tar.gz(r-4.5-noble)SpaCCI_1.0.3.tar.gz(r-4.4-noble)
SpaCCI_1.0.3.tgz(r-4.4-emscripten)
SpaCCI.pdf |SpaCCI.html✨
SpaCCI/json (API)
# Install 'SpaCCI' in R: |
install.packages('SpaCCI', repos = 'https://cloud.r-project.org') |
- 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
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:1aa475002f. Checks:3 OK. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Mar 20 2025 |
R-4.5-linux-x86_64 | OK | Mar 20 2025 |
R-4.4-linux-x86_64 | OK | Mar 20 2025 |
Exports:Find_regional_IDsGetShuffledCTGlobal_PermutationsLocal_Regional_PermutationsLR_databaseplot_localizedplot_localized_Seuratplot_SpaCCI_chordDiagramplot_SpaCCI_heatmapplot_SpaCCI_localplot_SpaCCI_local_Strengthplot_Strength_localizedplot_Strength_Seuratpossible_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.applygenericsggplot2ggrepelggridgesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenbaselifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmennlsopensslparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratSeuratObjectshapeshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo
Citation
To cite package ‘SpaCCI’ in publications use:
Ku L (2025). SpaCCI: Spatially Aware Cell-Cell Interaction Analysis. R package version 1.0.3, https://CRAN.R-project.org/package=SpaCCI.
Corresponding BibTeX entry:
@Manual{, title = {SpaCCI: Spatially Aware Cell-Cell Interaction Analysis}, author = {Li-Ting Ku}, year = {2025}, note = {R package version 1.0.3}, url = {https://CRAN.R-project.org/package=SpaCCI}, }