{
  "_id": "6a1032d8acfb0bcc41c97cfd",
  "Package": "STDistance",
  "Title": "Spatial Transcriptomics Distance Calculation and Visualization",
  "Version": "0.6.6",
  "Authors@R": "c(person(given = \"Zixiang\", family = \"Wang\",\nemail = \"wangzixiang@sdu.edu.cn\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5252-9764\")),\nperson(given = \"Lei\", family = \"Yang\",\nemail = \"970214035yl@gmail.com\",\nrole = \"aut\"),\nperson(given = \"Zhaojian\", family = \"Liu\",\nemail = \"liujian9782@sdu.edu.cn\",\nrole = \"aut\"))",
  "Description": "Analysis of spatial relationships between cell types in\nspatial transcriptomics data. Spatial proximity is a critical\nfactor in cell-cell communication. The package calculates\nnearest neighbor distances between specified cell types and\nprovides visualization tools to explore spatial patterns.\nApplications include studying cell-cell interactions, immune\nmicroenvironment characterization, and spatial organization of\ntissues.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-12 08:33:00 UTC",
    "User": "root"
  },
  "Author": "Zixiang Wang [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5252-9764>), Lei Yang [aut],\nZhaojian Liu [aut]",
  "Maintainer": "Zixiang Wang <wangzixiang@sdu.edu.cn>",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://princewang2018.r-universe.dev",
  "Date/Publication": "2025-07-22 13:00:55 UTC",
  "RemoteUrl": "https://github.com/cran/STDistance",
  "RemoteRef": "HEAD",
  "RemoteSha": "a22de12955b4a91a838bc77d87df1e8b9d341612",
  "MD5sum": "19413f47a2916257c2531a7b6b1ebbb3",
  "_user": "princewang2018",
  "_type": "src",
  "_file": "STDistance_0.6.6.tar.gz",
  "_fileid": "7b59755772944176aaab66c87bab4b1814f153dfb4d37343cc0a8f4d4014557c",
  "_filesize": 659079,
  "_sha256": "7b59755772944176aaab66c87bab4b1814f153dfb4d37343cc0a8f4d4014557c",
  "_created": "2026-05-12T08:33:00.000Z",
  "_published": "2026-05-22T10:41:28.597Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77363588995,
      "time": 155,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6939405493"
    },
    {
      "job": 77363589281,
      "time": 154,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6939405404"
    },
    {
      "job": 77363589345,
      "time": 175,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6939403924"
    },
    {
      "job": 77363589139,
      "time": 215,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6939406915"
    },
    {
      "job": 77363588517,
      "time": 210,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6939354336"
    },
    {
      "job": 77363588655,
      "time": 123,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7158573425"
    },
    {
      "job": 77363589361,
      "time": 149,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6939403772"
    },
    {
      "job": 77363589662,
      "time": 94,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6939386325"
    },
    {
      "job": 77363589307,
      "time": 93,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6939385654"
    }
  ],
  "_buildurl": "https://github.com/r-universe/princewang2018/actions/runs/25722860960",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/STDistance",
  "_commit": {
    "id": "a22de12955b4a91a838bc77d87df1e8b9d341612",
    "author": "Zixiang Wang <wangzixiang@sdu.edu.cn>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.6.6\n",
    "time": 1753189255
  },
  "_maintainer": {
    "name": "Zixiang Wang",
    "email": "wangzixiang@sdu.edu.cn",
    "login": "princewang2018",
    "orcid": "0000-0001-5252-9764",
    "uuid": 37299182
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "Hmisc",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-25",
      "n": 1
    },
    {
      "week": "2025-30",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.6.4",
      "date": "2025-06-18"
    },
    {
      "name": "0.6.6",
      "date": "2025-07-22"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "princewang2018",
      "count": 2,
      "uuid": 37299182
    }
  ],
  "_userbio": {
    "uuid": 37299182,
    "type": "user",
    "name": "Zixiang Wang",
    "description": "I love server‘s fans making noise."
  },
  "_downloads": {
    "count": 179,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/STDistance"
  },
  "_searchresults": 6,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/STDistance.html",
    "manual.pdf"
  ],
  "_realowner": "princewang2018",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.6.4",
      "date": "2025-06-18"
    },
    {
      "version": "0.6.6",
      "date": "2025-07-22"
    }
  ],
  "_exports": [
    "calculate_correlations",
    "calculate_nearest_distances",
    "normalize_spatial",
    "plot_distance_boxplot",
    "plot_radial_distance",
    "visualize_spatial_gradient",
    "visualize_spatial_multinetwork",
    "visualize_spatial_network"
  ],
  "_datasets": [
    {
      "name": "distance_results",
      "title": "distance_results",
      "object": "distance_results",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Newbarcode",
        "Epithelial_cells_A",
        "Epithelial_cells_B",
        "Epithelial_cells_C",
        "Epithelial_cells_D"
      ],
      "rows": 18,
      "table": true,
      "tojson": true
    },
    {
      "name": "metadata",
      "title": "Metadata",
      "object": "metadata",
      "class": [
        "data.frame"
      ],
      "fields": [
        "orig.ident",
        "nCount_Spatial",
        "nFeature_Spatial",
        "nCount_SCT",
        "nFeature_SCT",
        "integrated_snn_res.0.8",
        "seurat_clusters",
        "celltype_ABCDepi",
        "gen2_SPLIz_numeric"
      ],
      "rows": 293,
      "table": true,
      "tojson": true
    },
    {
      "name": "posi",
      "title": "posi",
      "object": "posi",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Newbarcode",
        "barcode",
        "in_tissue",
        "array_row",
        "array_col",
        "pxl_row_in_fullres",
        "pxl_col_in_fullres",
        "Sample",
        "Sampleid",
        "orig.ident",
        "nCount_Spatial",
        "nFeature_Spatial",
        "nCount_SCT",
        "nFeature_SCT",
        "integrated_snn_res.0.8",
        "seurat_clusters",
        "celltype_ABCDepi",
        "gen2_SPLIz_numeric"
      ],
      "rows": 293,
      "table": true,
      "tojson": true
    },
    {
      "name": "tissue_posi",
      "title": "tissue_posi",
      "object": "tissue_posi",
      "class": [
        "data.frame"
      ],
      "fields": [
        "barcode",
        "in_tissue",
        "array_row",
        "array_col",
        "pxl_row_in_fullres",
        "pxl_col_in_fullres",
        "Sample",
        "Sampleid",
        "Newbarcode"
      ],
      "rows": 9984,
      "table": true,
      "tojson": true
    },
    {
      "name": "tissue_posi_normalized",
      "title": "tissue_posi_normalized",
      "object": "tissue_posi_normalized",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "barcode",
        "in_tissue",
        "array_row",
        "array_col",
        "pxl_row_in_fullres",
        "pxl_col_in_fullres",
        "Sample",
        "Sampleid",
        "Newbarcode"
      ],
      "rows": 9984,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calculate_correlations",
      "title": "Perform correlation analysis between spatial features and distance metrics with visualization",
      "topics": [
        "calculate_correlations"
      ]
    },
    {
      "page": "calculate_nearest_distances",
      "title": "Calculate nearest distances between cell types",
      "topics": [
        "calculate_nearest_distances"
      ]
    },
    {
      "page": "distance_results",
      "title": "distance_results",
      "topics": [
        "distance_results"
      ]
    },
    {
      "page": "metadata",
      "title": "Metadata",
      "topics": [
        "metadata"
      ]
    },
    {
      "page": "normalize_spatial",
      "title": "Normalize spatial coordinates",
      "topics": [
        "normalize_spatial"
      ]
    },
    {
      "page": "plot_distance_boxplot",
      "title": "Visualize Nearest Neighbor Distances with Boxplot and Mean ± SEM",
      "topics": [
        "plot_distance_boxplot"
      ]
    },
    {
      "page": "plot_radial_distance",
      "title": "Radial Distance Visualization with Collision Avoidance",
      "topics": [
        "plot_radial_distance"
      ]
    },
    {
      "page": "posi",
      "title": "posi",
      "topics": [
        "posi"
      ]
    },
    {
      "page": "tissue_posi",
      "title": "tissue_posi",
      "topics": [
        "tissue_posi"
      ]
    },
    {
      "page": "tissue_posi_normalized",
      "title": "tissue_posi_normalized",
      "topics": [
        "tissue_posi_normalized"
      ]
    },
    {
      "page": "visualize_spatial_gradient",
      "title": "Visualize spatial network with expression gradient",
      "topics": [
        "visualize_spatial_gradient"
      ]
    },
    {
      "page": "visualize_spatial_multinetwork",
      "title": "Visualize spatial relationships between multiple cell types",
      "topics": [
        "visualize_spatial_multinetwork"
      ]
    },
    {
      "page": "visualize_spatial_network",
      "title": "Visualize spatial relationships between cell types",
      "topics": [
        "visualize_spatial_network"
      ]
    }
  ],
  "_readme": "https://github.com/cran/STDistance/raw/HEAD/README.md",
  "_rundeps": [
    "backports",
    "base64enc",
    "bslib",
    "cachem",
    "checkmate",
    "cli",
    "cluster",
    "colorspace",
    "cpp11",
    "data.table",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreign",
    "Formula",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "nnet",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "rlang",
    "rmarkdown",
    "rpart",
    "rstudioapi",
    "S7",
    "sass",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "my-vignette.Rmd",
      "filename": "my-vignette.html",
      "title": "STDistance - Spatial Transcriptomics Distance Calculation and Visualization",
      "author": "Zixiang Wang",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Description",
        "Installation",
        "Dependencies",
        "Input File Preparation",
        "Basic Workflow",
        "1. Load required packages and data",
        "2. Normalize spatial coordinates",
        "3. Merge spatial and metadata information",
        "4. Calculate nearest distances between cell types",
        "5. Compare distance among subgroups",
        "6. Create radial network visualization",
        "7. Spatial visualization of interactions",
        "8. Correlation analysis",
        "Applications",
        "Limitations",
        "Troubleshooting",
        "Citation",
        "Contact",
        "License"
      ],
      "created": "2025-06-18 13:04:06",
      "modified": "2025-06-18 13:04:06",
      "commits": 1
    }
  ],
  "_score": 3,
  "_indexed": true,
  "_nocasepkg": "stdistance",
  "_universes": [
    "princewang2018"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.6.6",
      "date": "2026-05-12T08:35:22.000Z",
      "distro": "noble",
      "commit": "a22de12955b4a91a838bc77d87df1e8b9d341612",
      "fileid": "e61f5f8deee293d7e18f1cda2f26b144775727a2d0fae107da6cdc0d13f54106",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/princewang2018/actions/runs/25722860960"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.6.6",
      "date": "2026-05-12T08:35:22.000Z",
      "distro": "noble",
      "commit": "a22de12955b4a91a838bc77d87df1e8b9d341612",
      "fileid": "d8be3e013a6f7776a22f12588352c72a1357710fd0d4974a5097ec2005ba61ed",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/princewang2018/actions/runs/25722860960"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.6.6",
      "date": "2026-05-12T08:35:25.000Z",
      "commit": "a22de12955b4a91a838bc77d87df1e8b9d341612",
      "fileid": "ee3d25a2a26fe855868d42391e59c633afb5dbc9d4ec14319e8400c4f6a2b0ca",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/princewang2018/actions/runs/25722860960"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.6.6",
      "date": "2026-05-12T08:35:21.000Z",
      "commit": "a22de12955b4a91a838bc77d87df1e8b9d341612",
      "fileid": "85640746785f8310481d55a778bad43f7a68493e457a61cba62a26de30c4cd3b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/princewang2018/actions/runs/25722860960"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.6.6",
      "date": "2026-05-12T08:35:16.000Z",
      "commit": "a22de12955b4a91a838bc77d87df1e8b9d341612",
      "fileid": "f0b49f99368f62621abc5b687750c7aceaebe7fb06f89b00a4343b12530deecf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/princewang2018/actions/runs/25722860960"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.6.6",
      "date": "2026-05-12T08:34:17.000Z",
      "commit": "a22de12955b4a91a838bc77d87df1e8b9d341612",
      "fileid": "95fca80c96a1c4841e92f1ac4696c68031b60c5e74963f9c474591bfb8524c69",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/princewang2018/actions/runs/25722860960"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.6.6",
      "date": "2026-05-12T08:34:17.000Z",
      "commit": "a22de12955b4a91a838bc77d87df1e8b9d341612",
      "fileid": "7306b7af6a7f90e187c43af5a9f0870d47b442d41f68a454283242cba6f1eba5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/princewang2018/actions/runs/25722860960"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.6.6",
      "date": "2026-05-22T10:41:09.000Z",
      "commit": "a22de12955b4a91a838bc77d87df1e8b9d341612",
      "fileid": "6f72ff1225b6f7d8cdfab62c4cbccee756febd8efd5b49cbfeb1d7df18e772eb",
      "status": "success",
      "buildurl": "https://github.com/r-universe/princewang2018/actions/runs/25722860960"
    }
  ]
}