{
  "_id": "6a1acbf81d7bb097a09de3ad",
  "Package": "hoodscanR",
  "Title": "Spatial cellular neighbourhood scanning in R",
  "Version": "1.11.0",
  "Authors@R": "c(person(given = \"Ning\",\nfamily = \"Liu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"ning.liu@adelaide.edu.au\",\ncomment = c(ORCID = \"0000-0002-9487-9305\")),\nperson(given = \"Jarryd\",\nfamily = \"Martin\",\nrole = c(\"aut\"),\nemail = \"\",\ncomment = c(ORCID = \"\")))",
  "Description": "hoodscanR is an user-friendly R package providing\nfunctions to assist cellular neighborhood analysis of any\nspatial transcriptomics data with single-cell resolution. All\nfunctions in the package are built based on the\nSpatialExperiment object, allowing integration into various\nspatial transcriptomics-related packages from Bioconductor. The\npackage can result in cell-level neighborhood annotation\noutput, along with funtions to perform neighborhood\ncolocalization analysis and neighborhood-based cell clustering.",
  "biocViews": "Spatial, Transcriptomics, SingleCell, Clustering",
  "License": "GPL-3 + file LICENSE",
  "URL": "https://github.com/DavisLaboratory/hoodscanR,\nhttps://davislaboratory.github.io/hoodscanR/",
  "BugReports": "https://github.com/DavisLaboratory/hoodscanR/issues",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libmagick++-dev gsfonts libicu-dev\nlibpng-dev libuv1-dev libssl-dev perl zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:29 UTC",
  "RemoteUrl": "https://github.com/bioc/hoodscanR",
  "RemoteRef": "HEAD",
  "RemoteSha": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-30 08:02:06 UTC",
    "User": "root"
  },
  "Author": "Ning Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-9487-9305>),\nJarryd Martin [aut]",
  "Maintainer": "Ning Liu <ning.liu@adelaide.edu.au>",
  "MD5sum": "b9b0363b0e8ee119a2b518f9e7b4b955",
  "_user": "bioc",
  "_type": "src",
  "_file": "hoodscanR_1.11.0.tar.gz",
  "_fileid": "6ba5372fbf1178bd1f5e2ef4b68f80884ecf37e08d0ba471855d1824efa5c68a",
  "_filesize": 2859410,
  "_sha256": "6ba5372fbf1178bd1f5e2ef4b68f80884ecf37e08d0ba471855d1824efa5c68a",
  "_created": "2026-05-30T08:02:06.000Z",
  "_published": "2026-05-30T11:37:28.270Z",
  "_jobs": [
    {
      "job": 78635274961,
      "time": 189,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306695772"
    },
    {
      "job": 78635274975,
      "time": 277,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306704451"
    },
    {
      "job": 78635274992,
      "time": 333,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306709986"
    },
    {
      "job": 78635274981,
      "time": 267,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306703571"
    },
    {
      "job": 78635274989,
      "time": 316,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306708302"
    },
    {
      "job": 78635274976,
      "time": 186,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307888070"
    },
    {
      "job": 78635274982,
      "time": 543,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306732840"
    },
    {
      "job": 78635274972,
      "time": 245,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307894293"
    },
    {
      "job": 78635274986,
      "time": 355,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306713727"
    },
    {
      "job": 78635055327,
      "time": 238,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306677739"
    },
    {
      "job": 78635274964,
      "time": 153,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306692469"
    },
    {
      "job": 78635274966,
      "time": 310,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306707735"
    },
    {
      "job": 78635274971,
      "time": 246,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306701270"
    },
    {
      "job": 78635274970,
      "time": 292,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306705973"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/hoodscanR",
  "_commit": {
    "id": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381289
  },
  "_maintainer": {
    "name": "Ning Liu",
    "email": "ning.liu@adelaide.edu.au",
    "login": "ningbioinfo",
    "linkedin": "in/ning-liu-437617157",
    "description": "Bioinformatician @ Polo Lab, Univ. of Adelaide · spatial & single-cell genomics, epigenomics, deep learning · standR / hoodscanR / scider",
    "uuid": 13725215,
    "orcid": "0000-0002-9487-9305"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Imports"
    },
    {
      "package": "SpatialExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "scico",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "RANN",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.9",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.11.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.10.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "spatial",
    "transcriptomics",
    "singlecell",
    "clustering",
    "cpp"
  ],
  "_stars": 13,
  "_contributors": [
    {
      "user": "ningbioinfo",
      "count": 48,
      "uuid": 13725215
    },
    {
      "user": "jwokaty",
      "count": 3,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 342,
    "source": "https://www.bioconductor.org/packages/stats/bioc/hoodscanR"
  },
  "_devurl": "https://github.com/davislaboratory/hoodscanr",
  "_pkgdown": "https://davislaboratory.github.io/hoodscanR/",
  "_searchresults": 37,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/hoodscanR.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/davislaboratory/hoodscanr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calcMetrics",
    "clustByHood",
    "findNearCells",
    "mergeByGroup",
    "mergeHoodSpe",
    "perplexityPermute",
    "plotColocal",
    "plotHoodMat",
    "plotProbDist",
    "plotTissue",
    "readHoodData",
    "scanHoods"
  ],
  "_datasets": [
    {
      "name": "spe",
      "title": "Example test spatial transcriptomics data",
      "object": "spe_test",
      "file": "spe_test.rda",
      "class": [
        "SpatialExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "calcMetrics",
      "title": "Calculate metrics for probability matrix",
      "topics": [
        "calcMetrics"
      ]
    },
    {
      "page": "clustByHood",
      "title": "Cluster the probability matrix with K-means",
      "topics": [
        "clustByHood",
        "clustByHood,matrix-method",
        "clustByHood,SpatialExperiment-method"
      ]
    },
    {
      "page": "findNearCells",
      "title": "Find the k-th nearest cells for each cell",
      "topics": [
        "findNearCells"
      ]
    },
    {
      "page": "mergeByGroup",
      "title": "Merge probability matrix based on annotations",
      "topics": [
        "mergeByGroup"
      ]
    },
    {
      "page": "mergeHoodSpe",
      "title": "Merge probability matrix into SpatialExperiment object.",
      "topics": [
        "mergeHoodSpe"
      ]
    },
    {
      "page": "perplexityPermute",
      "title": "Compute p-value for perplexity via permutation",
      "topics": [
        "perplexityPermute"
      ]
    },
    {
      "page": "plotColocal",
      "title": "Plot heatmap for neighbourhood analysis",
      "topics": [
        "plotColocal",
        "plotColocal,matrix-method",
        "plotColocal,SpatialExperiment-method"
      ]
    },
    {
      "page": "plotHoodMat",
      "title": "Plot probability matrix as a heatmap",
      "topics": [
        "plotHoodMat",
        "plotHoodMat,matrix-method",
        "plotHoodMat,SpatialExperiment-method"
      ]
    },
    {
      "page": "plotProbDist",
      "title": "Plot probability distribution",
      "topics": [
        "plotProbDist",
        "plotProbDist,matrix-method",
        "plotProbDist,SpatialExperiment-method"
      ]
    },
    {
      "page": "plotTissue",
      "title": "Plot cells based on cell position on tissue.",
      "topics": [
        "plotTissue"
      ]
    },
    {
      "page": "readHoodData",
      "title": "Read cellular position and annotation data into a list object.",
      "topics": [
        "readHoodData"
      ]
    },
    {
      "page": "scanHoods",
      "title": "Scan cellular neighbourhoods.",
      "topics": [
        "scanHoods"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/hoodscanR/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "base64enc",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "doParallel",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "fs",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggplot2",
    "GlobalOptions",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "httr2",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "purrr",
    "R6",
    "RANN",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "rjson",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scico",
    "Seqinfo",
    "shape",
    "SingleCellExperiment",
    "SparseArray",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XVector",
    "yaml"
  ],
  "_sysdeps": [
    {
      "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"
    }
  ],
  "_vignettes": [
    {
      "source": "Quick_start.Rmd",
      "filename": "Quick_start.html",
      "title": "A quick start guide to the hoodscanR package",
      "author": "Ning Liu, Melissa Davis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Quick start",
        "Data exploration",
        "Neighborhoods scanning",
        "Neighborhoods analysis",
        "Session info"
      ],
      "created": "2023-08-14 11:02:47",
      "modified": "2023-09-25 06:18:52",
      "commits": 4
    }
  ],
  "_score": 5.682145076373832,
  "_indexed": true,
  "_nocasepkg": "hoodscanr",
  "_universes": [
    "bioc",
    "ningbioinfo",
    "davislaboratory"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-30T08:05:00.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "54b4f555c2a5a1810067dfaf874b1f0dc6ffb43f4d3e37936076b4d50565ec71",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-30T08:05:20.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "fff3ad2e7149a87a178925982936666fa94bd81bf1702a2284d5bd17266df96f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-30T08:04:51.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "c2a8b7a9078bfced69e8d910e83484cce8654fb35986d28d48ad41413e64fa9a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-30T08:05:19.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "8c2e1b554c17845b4bff6d4c07c7e6b2d74e8e2bf2935273a7415191ebb1865a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-30T11:34:17.000Z",
      "arch": "aarch64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "318316ff267d426b2d77f214e7cc6043985bbdd93a9152a70dbe54000d937f1d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-30T08:07:08.000Z",
      "arch": "x86_64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "9f6693759ab7055a864ea9e5b5d102d9f101ac1ea97b6a742458e975b47f25d9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-30T11:34:36.000Z",
      "arch": "aarch64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "f183999ec18fff19c482294f017983f060364fd74f22e3c6c1ecd44ee1bfbead",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-30T08:05:24.000Z",
      "arch": "x86_64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "4a2bb6f2c8015888f01c3c6ee172e9aa91dc128d247392ef2a9a69db88ac4f6d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.11.0",
      "date": "2026-05-30T08:05:07.000Z",
      "arch": "emscripten",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "53ea8666c8e777ac62303379a09c423b80e2679ec0752971322111e07b0f6972",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-30T08:04:30.000Z",
      "arch": "x86_64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "c197386fdf2777d67a3f51e3e491c702963622357faaf87dfe8ea14525537d78",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-30T08:03:39.000Z",
      "arch": "x86_64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "96beb8e904c41c03b045c2124e68b0b6d48552ae8da7b5f00cbc4552aa397b77",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-30T08:03:56.000Z",
      "arch": "x86_64",
      "commit": "09a08af3e37d1309c4091e6baa8e41835f6f5696",
      "fileid": "9fa49d88895fc35c726d2bd3f33c46768633bb644a5c086fc04b6e26dfcf3824",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678657733"
    }
  ]
}