{
  "_id": "6acb3d7ffe5cc25786e8c933",
  "Package": "SpaTalk",
  "Title": "Spatially Resolved Cell-Cell Communication Inference for Spatial\nTranscriptomics",
  "Version": "2.0.0",
  "Authors@R": "c(\nperson(\"Zaoqu\", \"Liu\", , \"liuzaoqu@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0452-742X\")),\nperson(\"Xin\", \"Shao\", , \"xin_shao@zju.edu.cn\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-1928-3878\")))",
  "Description": "Infers spatially resolved cell-cell communications from\nspatial transcriptomics data using graph network and knowledge\ngraph approaches. Supports both single-cell resolution and\nspot-based spatial transcriptomics platforms. Provides cell\ntype deconvolution, ligand-receptor interaction analysis, and\ndownstream pathway inference.",
  "URL": "https://zaoqu-liu.github.io/SpaTalk/,\nhttps://github.com/Zaoqu-Liu/SpaTalk",
  "BugReports": "https://github.com/Zaoqu-Liu/SpaTalk/issues",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Remotes": [
    "linxihui/NNLM"
  ],
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev python3 libx11-dev zlib1g-dev",
  "Repository": "https://zaoqu-liu.r-universe.dev",
  "Date/Publication": "2026-01-23 13:41:43 UTC",
  "RemoteUrl": "https://github.com/Zaoqu-Liu/SpaTalk",
  "RemoteRef": "main",
  "RemoteSha": "a89213471656e1d7c846e47ed0ceab8e4348534e",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-09 11:06:12 UTC",
    "User": "root"
  },
  "Author": "Zaoqu Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-0452-742X>),\nXin Shao [aut] (ORCID: <https://orcid.org/0000-0002-1928-3878>)",
  "Maintainer": "Zaoqu Liu <liuzaoqu@163.com>",
  "_user": "zaoqu-liu",
  "_type": "src",
  "_file": "SpaTalk_2.0.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/c051d55c73533b5d26d25c7efd79a353fb1975cfd6896ae8d59314954cfea974",
  "_filesize": 5146963,
  "_sha256": "c051d55c73533b5d26d25c7efd79a353fb1975cfd6896ae8d59314954cfea974",
  "_expires": "2027-01-17T11:35:50.000Z",
  "_created": "2026-10-09T11:06:12.000Z",
  "_published": "2026-10-11T07:40:47.673Z",
  "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 114417986582,
      "time": 284,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11612472752"
    },
    {
      "job": 114417985963,
      "time": 352,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11612138957"
    },
    {
      "job": 114417986533,
      "time": 325,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11611699605"
    },
    {
      "job": 114417986439,
      "time": 340,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11611984183"
    },
    {
      "job": 114417985025,
      "time": 136,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 114417984907,
      "time": 340,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 114417985991,
      "time": 202,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11613985639"
    },
    {
      "job": 114417985884,
      "time": 457,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11612514478"
    },
    {
      "job": 114417985544,
      "time": 503,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11612670163"
    },
    {
      "job": 114417986154,
      "time": 220,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11612337665"
    },
    {
      "job": 114417986027,
      "time": 414,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11612597798"
    },
    {
      "job": 114417985581,
      "time": 364,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11612701408"
    },
    {
      "job": 114417984999,
      "time": 112,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 114417986384,
      "time": 409,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11611519639"
    },
    {
      "job": 114417986394,
      "time": 319,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11612766133"
    }
  ],
  "_upstream": "https://github.com/Zaoqu-Liu/SpaTalk",
  "_commit": {
    "id": "a89213471656e1d7c846e47ed0ceab8e4348534e",
    "author": "Zaoqu-Liu <liuzaoqu@163.com>",
    "committer": "Zaoqu-Liu <liuzaoqu@163.com>",
    "message": "Fix R-universe build: move NNLM to Suggests\n\n- NNLM is not on CRAN, R-universe cannot auto-install from Remotes\n- Move NNLM from Imports to Suggests\n- Add runtime check with helpful error message for NNLM\n- Regenerate NAMESPACE\n",
    "time": 1769175703
  },
  "_maintainer": {
    "name": "Zaoqu Liu",
    "email": "liuzaoqu@163.com",
    "login": "zaoqu-liu",
    "uuid": 68080738,
    "orcid": "0000-0002-0452-742X"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "ggalluvial",
      "role": "Depends"
    },
    {
      "package": "doParallel",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Seurat",
      "version": ">= 3.0.0",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "progress",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggExtra",
      "role": "Imports"
    },
    {
      "package": "crayon",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "scatterpie",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "corrplot",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "ggraph",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "iterators",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "digest",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "prettydoc",
      "role": "Suggests"
    },
    {
      "package": "NNLM",
      "role": "Suggests"
    },
    {
      "package": "spacexr",
      "role": "Suggests"
    },
    {
      "package": "SPOTlight",
      "role": "Suggests"
    },
    {
      "package": "deconvSeq",
      "role": "Suggests"
    },
    {
      "package": "reticulate",
      "role": "Suggests"
    },
    {
      "package": "anndata",
      "role": "Suggests"
    },
    {
      "package": "sceasy",
      "role": "Suggests"
    }
  ],
  "_owner": "zaoqu-liu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-04",
      "n": 8
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "zaoqu-liu",
      "count": 8,
      "uuid": 68080738
    }
  ],
  "_userbio": {
    "uuid": 68080738,
    "type": "user",
    "name": "LIU Zaoqu",
    "followers": 204,
    "description": "AI4S"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SpaTalk"
  },
  "_devurl": "https://github.com/zaoqu-liu/spatalk",
  "_pkgdown": "https://zaoqu-liu.github.io/SpaTalk/",
  "_searchresults": 39,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SpaTalk.html"
  ],
  "_cranurl": false,
  "_exports": [
    "cpp_batch_coexp",
    "cpp_batch_cor",
    "cpp_coexp_fast",
    "cpp_fast_dist",
    "cpp_fast_sampling",
    "cpp_knn",
    "cpp_permutation_test",
    "cpp_random_walk",
    "createSpaTalk",
    "dec_cci",
    "dec_cci_all",
    "dec_celltype",
    "demo_dec_result",
    "demo_geneinfo",
    "demo_lrpairs",
    "demo_pathways",
    "demo_sc_data",
    "demo_st_data",
    "demo_st_meta",
    "demo_st_sc_data",
    "demo_st_sc_meta",
    "find_lr_path",
    "generate_spot",
    "get_lr_path",
    "plot_ccdist",
    "plot_cci_lrpairs",
    "plot_lr_path",
    "plot_lrpair",
    "plot_lrpair_vln",
    "plot_path2gene",
    "plot_st_celltype",
    "plot_st_celltype_all",
    "plot_st_celltype_density",
    "plot_st_celltype_percent",
    "plot_st_cor_heatmap",
    "plot_st_gene",
    "plot_st_pie",
    "plot_st_pie_generate",
    "rev_gene",
    "set_expected_cell",
    "show"
  ],
  "_datasets": [
    {
      "name": "geneinfo",
      "title": "geneinfo",
      "object": "geneinfo",
      "class": [
        "data.frame"
      ],
      "fields": [
        "symbol",
        "synonyms",
        "species"
      ],
      "rows": 250934,
      "table": true,
      "tojson": true
    },
    {
      "name": "lrpairs",
      "title": "lrpairs",
      "object": "lrpairs",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ligand",
        "receptor",
        "species"
      ],
      "rows": 5427,
      "table": true,
      "tojson": true
    },
    {
      "name": "pathways",
      "title": "pathways",
      "object": "pathways",
      "class": [
        "data.frame"
      ],
      "fields": [
        "src",
        "dest",
        "pathway",
        "source",
        "type",
        "src_tf",
        "dest_tf",
        "species"
      ],
      "rows": 669197,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dot-use_cpp_permutation",
      "title": "Use Rcpp for fast permutation if available",
      "topics": [
        ".use_cpp_permutation"
      ]
    },
    {
      "page": "dot-use_cpp_random_walk",
      "title": "Use Rcpp for fast random walk if available",
      "topics": [
        ".use_cpp_random_walk"
      ]
    },
    {
      "page": "cpp_batch_coexp",
      "title": "Calculate co-expression for multiple gene pairs",
      "topics": [
        "cpp_batch_coexp"
      ]
    },
    {
      "page": "cpp_batch_cor",
      "title": "Calculate correlation between a vector and matrix columns",
      "topics": [
        "cpp_batch_cor"
      ]
    },
    {
      "page": "cpp_coexp_fast",
      "title": "Calculate co-expression ratios",
      "topics": [
        "cpp_coexp_fast"
      ]
    },
    {
      "page": "cpp_fast_dist",
      "title": "Calculate Euclidean distance matrix",
      "topics": [
        "cpp_fast_dist"
      ]
    },
    {
      "page": "cpp_fast_sampling",
      "title": "Sample cells to reconstruct spot expression",
      "topics": [
        "cpp_fast_sampling"
      ]
    },
    {
      "page": "cpp_knn",
      "title": "Find K nearest neighbors",
      "topics": [
        "cpp_knn"
      ]
    },
    {
      "page": "cpp_permutation_test",
      "title": "Permutation test for LR co-expression significance",
      "topics": [
        "cpp_permutation_test"
      ]
    },
    {
      "page": "cpp_random_walk",
      "title": "Random walk on gene-gene interaction network",
      "topics": [
        "cpp_random_walk"
      ]
    },
    {
      "page": "createSpaTalk",
      "title": "SpaTalk object",
      "topics": [
        "createSpaTalk"
      ]
    },
    {
      "page": "dec_cci",
      "title": "Decomposing cell-cell communications for spatial transciptomics data",
      "topics": [
        "dec_cci"
      ]
    },
    {
      "page": "dec_cci_all",
      "title": "Decomposing cell-cell communications for spatial transciptomics data",
      "topics": [
        "dec_cci_all"
      ]
    },
    {
      "page": "dec_celltype",
      "title": "Decomposing cell type for spatial transcriptomics data",
      "topics": [
        "dec_celltype"
      ]
    },
    {
      "page": "demo_dec_result",
      "title": "Demo data of dec_result",
      "topics": [
        "demo_dec_result"
      ]
    },
    {
      "page": "demo_geneinfo",
      "title": "Demo data of geneinfo",
      "topics": [
        "demo_geneinfo"
      ]
    },
    {
      "page": "demo_lrpairs",
      "title": "Demo data of lrpairs",
      "topics": [
        "demo_lrpairs"
      ]
    },
    {
      "page": "demo_pathways",
      "title": "Demo data of pathways",
      "topics": [
        "demo_pathways"
      ]
    },
    {
      "page": "demo_sc_data",
      "title": "Demo data of sc_data",
      "topics": [
        "demo_sc_data"
      ]
    },
    {
      "page": "demo_st_data",
      "title": "Demo data of st_data",
      "topics": [
        "demo_st_data"
      ]
    },
    {
      "page": "demo_st_meta",
      "title": "Demo data of st_meta",
      "topics": [
        "demo_st_meta"
      ]
    },
    {
      "page": "demo_st_sc_data",
      "title": "Demo data of single-cell st_data",
      "topics": [
        "demo_st_sc_data"
      ]
    },
    {
      "page": "demo_st_sc_meta",
      "title": "Demo data of st_sc_meta",
      "topics": [
        "demo_st_sc_meta"
      ]
    },
    {
      "page": "find_lr_path",
      "title": "Find lrpairs and pathways",
      "topics": [
        "find_lr_path"
      ]
    },
    {
      "page": "geneinfo",
      "title": "geneinfo",
      "topics": [
        "geneinfo"
      ]
    },
    {
      "page": "generate_spot",
      "title": "Generate pseudo spot st_data",
      "topics": [
        "generate_spot"
      ]
    },
    {
      "page": "get_lr_path",
      "title": "Get LR and downstream pathways",
      "topics": [
        "get_lr_path"
      ]
    },
    {
      "page": "lrpairs",
      "title": "lrpairs",
      "topics": [
        "lrpairs"
      ]
    },
    {
      "page": "pathways",
      "title": "pathways",
      "topics": [
        "pathways"
      ]
    },
    {
      "page": "plot_ccdist",
      "title": "Plot cell-cell distribution",
      "topics": [
        "plot_ccdist"
      ]
    },
    {
      "page": "plot_cci_lrpairs",
      "title": "Plot LR pairs",
      "topics": [
        "plot_cci_lrpairs"
      ]
    },
    {
      "page": "plot_lr_path",
      "title": "Plot LR and downstream pathways",
      "topics": [
        "plot_lr_path"
      ]
    },
    {
      "page": "plot_lrpair",
      "title": "Plot LR pair",
      "topics": [
        "plot_lrpair"
      ]
    },
    {
      "page": "plot_lrpair_vln",
      "title": "Plot spatial distance of LR pair with vlnplot",
      "topics": [
        "plot_lrpair_vln"
      ]
    },
    {
      "page": "plot_path2gene",
      "title": "River plot of significantly activated pathways and related downstream genes of receptors.",
      "topics": [
        "plot_path2gene"
      ]
    },
    {
      "page": "plot_st_celltype",
      "title": "Plot spatial distribution of a single cell type",
      "topics": [
        "plot_st_celltype"
      ]
    },
    {
      "page": "plot_st_celltype_all",
      "title": "Plot spatial distribution of all cell types",
      "topics": [
        "plot_st_celltype_all"
      ]
    },
    {
      "page": "plot_st_celltype_density",
      "title": "Plot spatial density of a single cell type",
      "topics": [
        "plot_st_celltype_density"
      ]
    },
    {
      "page": "plot_st_celltype_percent",
      "title": "Plot spatial distribution of a single cell type percent",
      "topics": [
        "plot_st_celltype_percent"
      ]
    },
    {
      "page": "plot_st_cor_heatmap",
      "title": "Plot heatpmap of correlation between marker genes and cell types",
      "topics": [
        "plot_st_cor_heatmap"
      ]
    },
    {
      "page": "plot_st_gene",
      "title": "Plot spatial distribution of gene",
      "topics": [
        "plot_st_gene"
      ]
    },
    {
      "page": "plot_st_pie",
      "title": "Plot spatial transcriptomics data",
      "topics": [
        "plot_st_pie"
      ]
    },
    {
      "page": "plot_st_pie_generate",
      "title": "Plot spatial transcriptomics data",
      "topics": [
        "plot_st_pie_generate"
      ]
    },
    {
      "page": "rev_gene",
      "title": "Pre-processing step: revising gene symbols",
      "topics": [
        "rev_gene"
      ]
    },
    {
      "page": "set_expected_cell",
      "title": "Set the expected cell",
      "topics": [
        "set_expected_cell"
      ]
    },
    {
      "page": "show-SpaTalk-method",
      "title": "Show SpaTalk object",
      "topics": [
        "show,SpaTalk-method"
      ]
    },
    {
      "page": "SpaTalk",
      "title": "Definition of 'SpaTalk' class",
      "topics": [
        "SpaTalk",
        "SpaTalk-class"
      ]
    }
  ],
  "_readme": "https://github.com/Zaoqu-Liu/SpaTalk/raw/main/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "bit",
    "bit64",
    "bitops",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "caTools",
    "circlize",
    "cli",
    "clipr",
    "cluster",
    "codetools",
    "colorspace",
    "colourpicker",
    "commonmark",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "deldir",
    "Deriv",
    "digest",
    "doBy",
    "doParallel",
    "dotCall64",
    "dplyr",
    "dqrng",
    "evaluate",
    "farver",
    "fastDummies",
    "fastmap",
    "fitdistrplus",
    "FNN",
    "fontawesome",
    "foreach",
    "forecast",
    "Formula",
    "fracdiff",
    "fs",
    "future",
    "future.apply",
    "generics",
    "ggalluvial",
    "ggExtra",
    "ggforce",
    "ggfun",
    "ggplot2",
    "ggpubr",
    "ggraph",
    "ggrepel",
    "ggridges",
    "ggsci",
    "ggsignif",
    "GlobalOptions",
    "globals",
    "glue",
    "goftest",
    "gplots",
    "graphlayouts",
    "gridExtra",
    "gtable",
    "gtools",
    "here",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "ica",
    "igraph",
    "irlba",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "listenv",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "miniUI",
    "minqa",
    "modelr",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "otel",
    "parallelly",
    "patchwork",
    "pbapply",
    "pbkrtest",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polyclip",
    "polynom",
    "prettyunits",
    "progress",
    "progressr",
    "promises",
    "purrr",
    "quantreg",
    "R6",
    "RANN",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppHNSW",
    "RcppProgress",
    "RcppThread",
    "RcppTOML",
    "Rdpack",
    "readr",
    "reformulas",
    "reshape2",
    "reticulate",
    "rlang",
    "rmarkdown",
    "ROCR",
    "rprojroot",
    "RSpectra",
    "rstatix",
    "Rtsne",
    "S7",
    "sass",
    "scales",
    "scattermore",
    "scatterpie",
    "sctransform",
    "Seurat",
    "SeuratObject",
    "shape",
    "shiny",
    "shinyjs",
    "sitmo",
    "sourcetools",
    "sp",
    "spam",
    "SparseM",
    "spatstat.data",
    "spatstat.explore",
    "spatstat.geom",
    "spatstat.random",
    "spatstat.sparse",
    "spatstat.univar",
    "spatstat.utils",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "systemfonts",
    "tensor",
    "tibble",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tinytex",
    "tweenr",
    "tzdb",
    "urca",
    "utf8",
    "uwot",
    "vctrs",
    "viridis",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "xtable",
    "yaml",
    "yulab.utils",
    "zoo"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "advanced.Rmd",
      "filename": "advanced.html",
      "title": "SpaTalk Advanced Usage",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Custom Databases",
        "Custom Ligand-Receptor Pairs",
        "Custom Pathway Database",
        "Alternative Deconvolution Methods",
        "Method 1: Built-in NNLM (Default)",
        "Method 2: RCTD (spacexr)",
        "Method 3: Seurat Integration",
        "Method 4: SPOTlight",
        "Method 5: deconvSeq",
        "Method 6: stereoscope (Python)",
        "Method 7: cell2location (Python)",
        "Parallel Processing",
        "Enabling Parallel Processing",
        "Memory Optimization",
        "Platform-Specific Workflows",
        "10x Visium",
        "Slide-seq",
        "STARmap / MERFISH (Single-cell resolution)",
        "Extracting Results",
        "LR Pair Results",
        "Downstream TF Scores",
        "Full CCI Network",
        "Troubleshooting",
        "Common Issues",
        "Best Practices",
        "Session Info"
      ],
      "created": "2026-01-23 11:41:42",
      "modified": "2026-01-23 11:41:42",
      "commits": 1
    },
    {
      "source": "algorithm.Rmd",
      "filename": "algorithm.html",
      "title": "SpaTalk Algorithm: Methodological Framework",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Algorithmic Pipeline",
        "1. Cell-Type Deconvolution",
        "Mathematical Formulation",
        "NNLM Algorithm",
        "2. Spatial Reconstruction",
        "Monte Carlo Spatial Sampling",
        "k-Nearest Neighbor Mapping",
        "3. Knowledge Graph Integration",
        "LR-Pathway Database",
        "Pathway Filtering Algorithm",
        "4. Cell-Cell Communication Inference",
        "Co-expression Score",
        "Permutation Test",
        "5. Downstream Pathway Scoring",
        "Random Walk Algorithm",
        "C++ Implementation",
        "Computational Complexity",
        "References",
        "Session Info"
      ],
      "created": "2026-01-23 11:41:42",
      "modified": "2026-01-23 11:41:42",
      "commits": 1
    },
    {
      "source": "platforms.Rmd",
      "filename": "platforms.html",
      "title": "SpaTalk for Different Spatial Transcriptomics Platforms",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Single-Cell Resolution Platforms",
        "STARmap Example (Built-in Data)",
        "Other Single-Cell Platforms",
        "Spot-Based Platforms",
        "10x Visium Workflow",
        "Slide-seq / Slide-seqV2",
        "Workflow Comparison",
        "Single-cell Workflow (STARmap, MERFISH, Xenium)",
        "Spot-based Workflow (Visium, Slide-seq)",
        "Parameter Guidelines by Platform",
        "Best Practices",
        "For Spot-based Data",
        "For Single-cell Data",
        "Session Info"
      ],
      "created": "2026-01-23 11:41:42",
      "modified": "2026-01-23 12:00:15",
      "commits": 2
    },
    {
      "source": "visualization.Rmd",
      "filename": "visualization.html",
      "title": "SpaTalk Visualization Guide",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Setup",
        "Spatial Cell Type Visualization",
        "plot_st_celltype_all",
        "plot_st_celltype",
        "plot_st_celltype_density",
        "Gene Expression Visualization",
        "plot_st_gene",
        "Advanced Visualizations (After CCI Analysis)",
        "plot_ccdist",
        "plot_lrpair",
        "Customization Tips",
        "Custom Themes",
        "Summary of Visualization Functions",
        "Session Info"
      ],
      "created": "2026-01-23 11:41:42",
      "modified": "2026-01-23 12:00:15",
      "commits": 2
    },
    {
      "source": "SpaTalk.Rmd",
      "filename": "SpaTalk.html",
      "title": "SpaTalk: Quick Start Guide",
      "author": "Zaoqu Liu, Xin Shao",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Citation",
        "Key Features",
        "Installation",
        "Quick Start with STARmap Data",
        "Step 1: Load Package and Data",
        "Step 2: Create SpaTalk Object",
        "Step 3: Visualize Spatial Distribution",
        "Step 4: Filter LR-Pathway Pairs",
        "Step 5: Infer Cell-Cell Communications",
        "Step 6: Visualize Results",
        "Cell-Cell Distance Distribution",
        "LR Pair Spatial Distribution",
        "Next Steps",
        "Session Info"
      ],
      "created": "2026-01-23 11:41:42",
      "modified": "2026-01-23 12:00:15",
      "commits": 2
    }
  ],
  "_score": 3.9890046156985366,
  "_indexed": true,
  "_nocasepkg": "spatalk",
  "_universes": [
    "zaoqu-liu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.0.0",
      "date": "2026-10-09T11:10:15.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/2babd45770f06a4bd020c35cf8cbffb79c61d2162a4d67d70d02da78453bc612",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.0.0",
      "date": "2026-10-09T11:10:59.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/003e98a83b1f79896545777f74f65ad5fe8a8ffe3516bdd9a18cb9f0067b7d5b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.0.0",
      "date": "2026-10-09T11:11:00.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/e35f4ab6beb910e892ea87c5383372891dd6ef3acce850e85a50b81452e0fdc6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.0.0",
      "date": "2026-10-09T11:10:54.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/8b7e8db1e831e0e8ea4e7ecdc78548f2dfd71fda70877564a3f98088339c20b0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.0.0",
      "date": "2026-10-09T11:32:48.000Z",
      "arch": "aarch64",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/102589e140f6ae32080632ed3fbf9f86876c63956a9a8a660dabe926193bc855",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.0.0",
      "date": "2026-10-09T11:21:04.000Z",
      "arch": "x86_64",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/43b304f89f9182c9c88b005926cd925ef58bc54fb2836f126f8ec3c13d651491",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.0.0",
      "date": "2026-10-09T11:10:45.000Z",
      "arch": "emscripten",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/4aaab8716a77cf795c64d939cf5b9103d03bcffc7ef237141472cd3559375411",
      "status": "success",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.0.0",
      "date": "2026-10-09T11:11:58.000Z",
      "arch": "aarch64",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/3b2072ded13c7c1bdba99e7b9fbd468c9d2b27c255dab746f0074cfaa92fce30",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.0.0",
      "date": "2026-10-09T11:10:02.000Z",
      "arch": "x86_64",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/a6b47adb896f5bb0609db10463f385b550f8422355e06e3de806782a78b32cb6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.0.0",
      "date": "2026-10-09T11:11:56.000Z",
      "arch": "aarch64",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/f1aa3c64b68469ef337dc47f40f2a2725a29c4fd481959dd985a5bd8900deb5b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.0.0",
      "date": "2026-10-09T11:09:58.000Z",
      "arch": "x86_64",
      "commit": "a89213471656e1d7c846e47ed0ceab8e4348534e",
      "fileid": "https://r2.ropensci.org/ff5154a58a7e5fd8d326601e6c7f53fa86616facadaac22cd2740b91dbd736d7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/37920878716"
    }
  ]
}