{
  "_id": "6a19ed851d7bb097a09c8170",
  "Package": "SpaTopic",
  "Type": "Package",
  "Title": "Topic Inference to Identify Tissue Architecture in Multiplexed\nImages",
  "Version": "1.3.1",
  "Date": "2026-05-27",
  "Authors@R": "c(\nperson(\"Xiyu\", \"Peng\", email = \"pansypeng124@gmail.com\",\nrole = c(\"aut\", \"cre\"),comment = c(ORCID = \"0000-0003-4232-0910\")),\nperson(\"Nikki\", \"Xiao\", email = \"xmq041117@gmail.com\",\nrole = c(\"aut\"))\n)",
  "Description": "A novel spatial topic model to integrate both cell type\nand spatial information to identify the complex spatial tissue\narchitecture on multiplexed tissue images without human\nintervention. The Package implements a collapsed Gibbs sampling\nalgorithm for inference. The method is highly scalable to\nlarge-scale image datasets without extracting neighborhood\ninformation for every single cell. The package supports\nspatially resolved cell-level data analysis, topic inference,\nvisualization, and downstream biological interpretation of\ntissue microenvironments.",
  "License": "GPL (>= 3)",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "URL": "https://xiyupeng.github.io/SpaTopic/,\nhttps://github.com/xiyupeng/SpaTopic,\nhttps://doi.org/10.1038/s41467-025-61821-y",
  "BugReports": "https://github.com/xiyupeng/SpaTopic/issues",
  "Language": "en-US",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 19:44:25 UTC",
    "User": "root"
  },
  "Author": "Xiyu Peng [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4232-0910>), Nikki Xiao [aut]",
  "Maintainer": "Xiyu Peng <pansypeng124@gmail.com>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-05-29 15:00:02 UTC",
  "RemoteUrl": "https://github.com/cran/SpaTopic",
  "RemoteRef": "HEAD",
  "RemoteSha": "f7e1081eb1f9eb9550ca1e72d1dbe90de0af8486",
  "MD5sum": "3da4b10071477366efaa1dbb9a186293",
  "_user": "cran",
  "_type": "src",
  "_file": "SpaTopic_1.3.1.tar.gz",
  "_fileid": "2b8969730a37d32cbf9a304a08b84a199cb9e194d088d90bdfa65e19622f9030",
  "_filesize": 594859,
  "_sha256": "2b8969730a37d32cbf9a304a08b84a199cb9e194d088d90bdfa65e19622f9030",
  "_created": "2026-05-29T19:44:25.000Z",
  "_published": "2026-05-29T19:48:21.353Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78574883759,
      "time": 185,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7299652532"
    },
    {
      "job": 78574883758,
      "time": 183,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7299651588"
    },
    {
      "job": 78574883774,
      "time": 156,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299643456"
    },
    {
      "job": 78574883747,
      "time": 173,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299648863"
    },
    {
      "job": 78574126135,
      "time": 285,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299595635"
    },
    {
      "job": 78574883721,
      "time": 142,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7299639269"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/26658294208",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/SpaTopic",
  "_commit": {
    "id": "f7e1081eb1f9eb9550ca1e72d1dbe90de0af8486",
    "author": "Xiyu Peng <pansypeng124@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.3.1\n",
    "time": 1780066802
  },
  "_maintainer": {
    "name": "Xiyu Peng",
    "email": "pansypeng124@gmail.com",
    "login": "xiyupeng",
    "description": "biostatistics/bioinformatics",
    "uuid": 23034624,
    "orcid": "0000-0003-4232-0910"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "RcppProgress",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "Imports"
    },
    {
      "package": "RANN",
      "version": ">= 2.6.0",
      "role": "Imports"
    },
    {
      "package": "sf",
      "version": ">= 1.0-12",
      "role": "Imports"
    },
    {
      "package": "methods",
      "version": ">= 3.4",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "version": ">= 1.5.0",
      "role": "Imports"
    },
    {
      "package": "iterators",
      "version": ">= 1.0",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "SeuratObject",
      "version": ">= 4.9.9.9086",
      "role": "Suggests"
    },
    {
      "package": "doParallel",
      "version": ">= 1.0",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-22",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.3.1",
      "date": "2026-05-29"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "xiyupeng",
      "count": 4,
      "uuid": 23034624
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 174,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SpaTopic"
  },
  "_devurl": "https://github.com/xiyupeng/spatopic",
  "_pkgdown": "https://xiyupeng.github.io/SpaTopic/",
  "_searchresults": 22,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/SpaTopic.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/xiyupeng/spatopic",
  "_realowner": "xiyupeng",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2024-01-17"
    },
    {
      "version": "1.1.0",
      "date": "2024-04-23"
    },
    {
      "version": "1.2.0",
      "date": "2025-03-03"
    },
    {
      "version": "1.3.1",
      "date": "2026-05-29"
    }
  ],
  "_exports": [
    "frex_topic",
    "label_topics",
    "lift_topic",
    "prob_topic",
    "score_topic",
    "Seurat5obj_to_SpaTopic",
    "SpaTopic_inference",
    "stratified_sampling_3D_via_2D",
    "stratified_sampling_sf"
  ],
  "_datasets": [
    {
      "name": "lung5",
      "title": "Example input data for 'SpaTopic'",
      "object": "lung5",
      "class": [
        "data.frame"
      ],
      "fields": [
        "image",
        "X",
        "Y",
        "type"
      ],
      "rows": 100149,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "frex_topic",
      "title": "Calculate FREX ranked words and values for a topic",
      "topics": [
        "frex_topic"
      ]
    },
    {
      "page": "label_topics",
      "title": "Label topics function",
      "topics": [
        "label_topics"
      ]
    },
    {
      "page": "lift_topic",
      "title": "Calculate lift ranked words and values for a topic",
      "topics": [
        "lift_topic"
      ]
    },
    {
      "page": "lung5",
      "title": "Example input data for 'SpaTopic'",
      "topics": [
        "lung5"
      ]
    },
    {
      "page": "print.SpaTopic",
      "title": "Print method for SpaTopic objects",
      "topics": [
        "print.SpaTopic"
      ]
    },
    {
      "page": "prob_topic",
      "title": "Calculate highest probability words and values for a topic",
      "topics": [
        "prob_topic"
      ]
    },
    {
      "page": "score_topic",
      "title": "Calculate score ranked words and values for a topic",
      "topics": [
        "score_topic"
      ]
    },
    {
      "page": "Seurat5obj_to_SpaTopic",
      "title": "Convert a Seurat v5 object as the input of 'SpaTopic'",
      "topics": [
        "Seurat5obj_to_SpaTopic"
      ]
    },
    {
      "page": "SpaTopic_inference",
      "title": "'SpaTopic': fast topic inference to identify tissue architecture in multiplexed images",
      "topics": [
        "SpaTopic_inference"
      ]
    },
    {
      "page": "spatopic_message",
      "title": "Format messages for SpaTopic package",
      "topics": [
        "spatopic_message"
      ]
    },
    {
      "page": "SpaTopic-class",
      "title": "A class of the output from 'SpaTopic'",
      "topics": [
        "SpaTopic-class"
      ]
    },
    {
      "page": "SpaTopic-Package",
      "title": "SpaTopic: Spatial Topic Modeling for Multiplexed Images",
      "topics": [
        "SpaTopic-package",
        "SpaTopic",
        "SpaTopic-Package"
      ]
    },
    {
      "page": "stratified_sampling_3D_via_2D",
      "title": "Spatially stratified random sample points from a 3D image using 2D slicing.",
      "topics": [
        "stratified_sampling_3D_via_2D"
      ]
    },
    {
      "page": "stratified_sampling_sf",
      "title": "Spatially stratified random sample points from an image.",
      "topics": [
        "stratified_sampling_sf"
      ]
    }
  ],
  "_readme": "https://github.com/cran/SpaTopic/raw/HEAD/README.md",
  "_rundeps": [
    "class",
    "classInt",
    "codetools",
    "DBI",
    "e1071",
    "foreach",
    "iterators",
    "KernSmooth",
    "MASS",
    "proxy",
    "RANN",
    "Rcpp",
    "RcppArmadillo",
    "RcppProgress",
    "s2",
    "sf",
    "units",
    "wk"
  ],
  "_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"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "Intro_SpaTopic.Rmd",
      "filename": "Intro_SpaTopic.html",
      "title": "SpaTopic Basics",
      "author": "Xiyu Peng",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Simple Usage"
      ],
      "created": "2024-01-18 02:39:47",
      "modified": "2025-03-03 17:00:09",
      "commits": 3
    }
  ],
  "_score": 3.041392685158225,
  "_indexed": false,
  "_nocasepkg": "spatopic",
  "_universes": [
    "cran"
  ],
  "_indexurl": "https://xiyupeng.r-universe.dev/SpaTopic",
  "_previous": "1.2.0",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.1",
      "date": "2026-05-29T19:47:30.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "f7e1081eb1f9eb9550ca1e72d1dbe90de0af8486",
      "fileid": "4af66a7f169b3a94bb162219fa0b15cf4d268e2247029b6d90a705fa22d599a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26658294208"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.1",
      "date": "2026-05-29T19:47:26.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "f7e1081eb1f9eb9550ca1e72d1dbe90de0af8486",
      "fileid": "6bdf7137143477a6ba5d8270520e7575426d82c3d1260b488f424a926f9e0183",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26658294208"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.1",
      "date": "2026-05-29T19:46:57.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "f7e1081eb1f9eb9550ca1e72d1dbe90de0af8486",
      "fileid": "2756e919a660e6c4edc772c34ebd4df118cf78fbdae95a3d0d53877a215ab8a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26658294208"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.1",
      "date": "2026-05-29T19:47:19.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "f7e1081eb1f9eb9550ca1e72d1dbe90de0af8486",
      "fileid": "d72a0347c495f7e43cf4fe83c5511c0e85d877f26a835d800c30528f894c5955",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26658294208"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.1",
      "date": "2026-05-29T19:47:09.000Z",
      "arch": "emscripten",
      "commit": "f7e1081eb1f9eb9550ca1e72d1dbe90de0af8486",
      "fileid": "93113e46cd554fb104761b37d0583a870c2f9607118ec46c7117c943792fa44b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26658294208"
    }
  ]
}