{ "_id": "6a17edd9acfb0bcc41da50d7", "Package": "SpaCCI", "Type": "Package", "Title": "Spatially Aware Cell-Cell Interaction Analysis", "Version": "1.0.5", "Date": "2026-02-26", "Authors@R": "person(given = \"Li-Ting\",\nfamily = \"Ku\",\nrole = c(\"aut\", \"cre\"),\nemail = \"lku@mdanderson.org\")", "Maintainer": "Li-Ting Ku ", "Description": "Provides tools for analyzing spatial cell-cell\ninteractions based on ligand-receptor pairs, including\nfunctions for local, regional, and global analysis using\nspatial transcriptomics data. Integrates with databases like\n'CellChat' ,\n'CellPhoneDB' , 'Cellinker'\n, 'ICELLNET'\n, and 'ConnectomeDB'\n to\nidentify ligand-receptor pairs, visualize interactions through\nheatmaps, chord diagrams, and infer interactions on different\nspatial scales.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-28 07:09:15 UTC", "User": "root" }, "Author": "Li-Ting Ku [aut, cre]", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-02-27 08:30:23 UTC", "RemoteUrl": "https://github.com/cran/SpaCCI", "RemoteRef": "HEAD", "RemoteSha": "5d366077cdd40bf954a165fc2c1dfe115e3657df", "MD5sum": "58cecfbc3b3cc5e2e1fb4d41c27f0719", "_user": "cran", "_type": "src", "_file": "SpaCCI_1.0.5.tar.gz", "_fileid": "91be2b25b3ce574f7d7bf520936a419efd152b600ec70ce523c72114fa839052", "_filesize": 5162121, "_sha256": "91be2b25b3ce574f7d7bf520936a419efd152b600ec70ce523c72114fa839052", "_created": "2026-05-28T07:09:15.000Z", "_published": "2026-05-28T07:25:13.442Z", "_distro": "noble", "_jobs": [ { "job": 78241305925, "time": 895, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7260012848" }, { "job": 78241305862, "time": 258, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7259826421" }, { "job": 78241306079, "time": 259, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7259826772" }, { "job": 78241305966, "time": 263, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7259827622" }, { "job": 78240756379, "time": 258, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7259758157" }, { "job": 78241305852, "time": 226, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7259817982" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26560078354", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/SpaCCI", "_commit": { "id": "5d366077cdd40bf954a165fc2c1dfe115e3657df", "author": "Li-Ting Ku ", "committer": "cran-robot ", "message": "version 1.0.5\n", "time": 1772181023 }, "_maintainer": { "name": "Li-Ting Ku", "email": "lku@mdanderson.org" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.13", "role": "Imports" }, { "package": "Seurat", "version": ">= 4.0.0", "role": "Imports" }, { "package": "nnls", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "circlize", "version": ">= 0.4.12", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "FNN", "role": "Imports" }, { "package": "rlang", "role": "Imports" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-09", "n": 1 } ], "_tags": [ { "name": "1.0.5", "date": "2026-02-27" } ], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 180, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SpaCCI" }, "_searchresults": 22, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/SpaCCI.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2024-09-30" }, { "version": "1.0.2", "date": "2024-10-24" }, { "version": "1.0.3", "date": "2025-01-18" }, { "version": "1.0.4", "date": "2025-05-12" }, { "version": "1.0.5", "date": "2026-02-27" } ], "_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" ], "_datasets": [ { "name": "result_global", "title": "result_global data for SpaCCI", "object": "result_global", "file": "result_global.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "result_local", "title": "result_local data and spatial coordinates for SpaCCI Local Regional Data", "object": "result_local", "file": "result_local.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "result_local_spatial_coords_df", "title": "Local Spatial Coordinates Data Frame", "object": "result_local_spatial_coords_df", "file": "result_local_spatial_coords_df.rda", "class": [ "data.frame" ], "fields": [ "imagecol", "imagerow", "Spot_ID" ], "rows": 782, "table": true, "tojson": true }, { "name": "result_regional", "title": "result_regional data for SpaCCI", "object": "result_regional", "file": "result_regional.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "test_data", "title": "Test data for SpaCCI", "object": "test_data", "file": "test_data.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "Find_regional_IDs", "title": "Find the spatial neighborhood Spot IDs", "topics": [ "Find_regional_IDs" ] }, { "page": "GetShuffledCT", "title": "Perform a Deranged Shuffle of Cell Types", "topics": [ "GetShuffledCT" ] }, { "page": "Global_Permutations", "title": "Perform Global Permutations", "topics": [ "Global_Permutations" ] }, { "page": "Local_Regional_Permutations", "title": "Perform Local and Regional Permutations", "topics": [ "Local_Regional_Permutations" ] }, { "page": "LR_database", "title": "Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication", "topics": [ "LR_database" ] }, { "page": "plot_localized", "title": "Plot Localized Hotspot Pattern", "topics": [ "plot_localized" ] }, { "page": "plot_localized_Seurat", "title": "Plot Localized Hotspot Pattern on Seurat Object", "topics": [ "plot_localized_Seurat" ] }, { "page": "plot_SpaCCI_chordDiagram", "title": "Plot SpaCCI Results on Chord Diagram", "topics": [ "plot_SpaCCI_chordDiagram" ] }, { "page": "plot_SpaCCI_heatmap", "title": "Plot SpaCCI Results on the heatmap Visualize inferred significant cell-cell interactions using a heatmap", "topics": [ "plot_SpaCCI_heatmap" ] }, { "page": "plot_SpaCCI_local", "title": "Plot SpaCCI Localized Interaction Results", "topics": [ "plot_SpaCCI_local" ] }, { "page": "plot_SpaCCI_local_Strength", "title": "Plot SpaCCI Localized Interaction Strength Results", "topics": [ "plot_SpaCCI_local_Strength" ] }, { "page": "plot_Strength_localized", "title": "Plot Localized Hotspot Strength Pattern", "topics": [ "plot_Strength_localized" ] }, { "page": "plot_Strength_Seurat", "title": "Plot Localized Hotspot Strength Pattern on Seurat Object", "topics": [ "plot_Strength_Seurat" ] }, { "page": "possible_L_R_pairs_cellchat", "title": "CellChat Database: Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication", "topics": [ "possible_L_R_pairs_cellchat" ] }, { "page": "possible_L_R_pairs_Cellinker", "title": "Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication", "topics": [ "possible_L_R_pairs_Cellinker" ] }, { "page": "possible_L_R_pairs_cellphoneDB", "title": "Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication", "topics": [ "possible_L_R_pairs_cellphoneDB" ] }, { "page": "possible_L_R_pairs_connectome", "title": "Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication", "topics": [ "possible_L_R_pairs_connectome" ] }, { "page": "possible_L_R_pairs_ICELLNET", "title": "Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication", "topics": [ "possible_L_R_pairs_ICELLNET" ] }, { "page": "random_region", "title": "Select Closest Spatial IDs to a Center Point: this is used for permutation", "topics": [ "random_region" ] }, { "page": "result_global", "title": "result_global data for SpaCCI", "topics": [ "result_global" ] }, { "page": "result_local", "title": "result_local data and spatial coordinates for SpaCCI Local Regional Data", "topics": [ "result_local" ] }, { "page": "result_local_spatial_coords_df", "title": "Local Spatial Coordinates Data Frame", "topics": [ "result_local_spatial_coords_df" ] }, { "page": "result_regional", "title": "result_regional data for SpaCCI", "topics": [ "result_regional" ] }, { "page": "run_SpaCCI", "title": "Run SpaCCI Analysis", "topics": [ "run_SpaCCI" ] }, { "page": "scPalette", "title": "Generate a Color Palette", "topics": [ "scPalette" ] }, { "page": "SpaCCI_global", "title": "Infer Cell-Cell Interactions on a Global Scale", "topics": [ "SpaCCI_global" ] }, { "page": "SpaCCI_local", "title": "Infer Cell-Cell Interactions on a Local Scale", "topics": [ "SpaCCI_local" ] }, { "page": "SpaCCI_region", "title": "Infer Cell-Cell Interactions in a Specified Region", "topics": [ "SpaCCI_region" ] }, { "page": "test_data", "title": "Test data for SpaCCI", "topics": [ "test_data" ] } ], "_rundeps": [ "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" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 1.3424226808222062, "_indexed": true, "_nocasepkg": "spacci", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.5", "date": "2026-05-28T07:23:16.000Z", "distro": "noble", "arch": "aarch64", "commit": "5d366077cdd40bf954a165fc2c1dfe115e3657df", "fileid": "f72eec640fb4dfddeb22523a6edb84b643579a3859c4b655d8e624df73a068ca", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26560078354" }, { "r": "4.7.0", "os": "linux", "version": "1.0.5", "date": "2026-05-28T07:12:34.000Z", "distro": "noble", "arch": "x86_64", "commit": "5d366077cdd40bf954a165fc2c1dfe115e3657df", "fileid": "68c86ad2744a4b3b32810dc2205c5fcfb917f4cab6e627a637c594c625106eb5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26560078354" }, { "r": "4.6.0", "os": "linux", "version": "1.0.5", "date": "2026-05-28T07:12:49.000Z", "distro": "noble", "arch": "aarch64", "commit": "5d366077cdd40bf954a165fc2c1dfe115e3657df", "fileid": "2464ae7a332fe38fcb2aeb10b2c83e1a9867959b3edd38f53e7c8c68b5f22603", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26560078354" }, { "r": "4.6.0", "os": "linux", "version": "1.0.5", "date": "2026-05-28T07:12:38.000Z", "distro": "noble", "arch": "x86_64", "commit": "5d366077cdd40bf954a165fc2c1dfe115e3657df", "fileid": "c7ac4b4a61f8f56bb04d57d3d30ed6677b4e131008d1aeb625e9249db019a3a6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26560078354" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.5", "date": "2026-05-28T07:13:36.000Z", "arch": "emscripten", "commit": "5d366077cdd40bf954a165fc2c1dfe115e3657df", "fileid": "20767d99b172556577b810b93176a3323c98844027acc7a0d49a00e227d187e5", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26560078354" } ] }