{
  "_id": "6a1b088b1d7bb097a0a05154",
  "Package": "SpatialCPie",
  "Title": "Cluster analysis of Spatial Transcriptomics data",
  "Version": "1.28.0",
  "Authors@R": "person(\n\"Joseph\", \"Bergenstraahle\",\nemail = \"joseph.bergenstrahle@gmail.com\",\nrole = c(\"aut\", \"cre\")\n)",
  "Description": "SpatialCPie is an R package designed to facilitate cluster\nevaluation for spatial transcriptomics data by providing\nintuitive visualizations that display the relationships between\nclusters in order to guide the user during cluster\nidentification and other downstream applications. The package\nis built around a shiny \"gadget\" to allow the exploration of\nthe data with multiple plots in parallel and an interactive UI.\nThe user can easily toggle between different cluster\nresolutions in order to choose the most appropriate visual\ncues.",
  "biocViews": "Transcriptomics, Clustering, RNASeq, Software",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "6.1.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libx11-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:18 UTC",
  "RemoteUrl": "https://github.com/bioc/SpatialCPie",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "0234b14f0bd2a4a9c44b522a893184c29088fc90",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 10:59:02 UTC",
    "User": "root"
  },
  "Author": "Joseph Bergenstraahle [aut, cre]",
  "Maintainer": "Joseph Bergenstraahle <joseph.bergenstrahle@gmail.com>",
  "MD5sum": "58308779bb6135b3ea14e8626a9f5ccb",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "SpatialCPie_1.28.0.tar.gz",
  "_fileid": "2b816fc653b42cd1c395763dae78a1fd8534c19dbfc6a25fdcc88f4f5816a8e3",
  "_filesize": 911073,
  "_sha256": "2b816fc653b42cd1c395763dae78a1fd8534c19dbfc6a25fdcc88f4f5816a8e3",
  "_created": "2026-05-30T10:59:02.000Z",
  "_published": "2026-05-30T15:55:55.051Z",
  "_jobs": [
    {
      "job": 78644200887,
      "time": 196,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307744295"
    },
    {
      "job": 78644200901,
      "time": 295,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307752991"
    },
    {
      "job": 78644200900,
      "time": 348,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307757523"
    },
    {
      "job": 78644200892,
      "time": 178,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7309422803"
    },
    {
      "job": 78644200886,
      "time": 193,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7309423987"
    },
    {
      "job": 78643744678,
      "time": 282,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307692622"
    },
    {
      "job": 78644200893,
      "time": 149,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307740132"
    },
    {
      "job": 78644200896,
      "time": 553,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307776193"
    },
    {
      "job": 78644200894,
      "time": 561,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307776392"
    },
    {
      "job": 78644200903,
      "time": 200,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307745092"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680861812",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SpatialCPie",
  "_commit": {
    "id": "0234b14f0bd2a4a9c44b522a893184c29088fc90",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380558
  },
  "_maintainer": {
    "name": "Joseph Bergenstraahle",
    "email": "joseph.bergenstrahle@gmail.com",
    "login": "jbergenstrahle",
    "description": "",
    "uuid": 8091989
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "colorspace",
      "version": ">= 1.3-2",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.12.2",
      "role": "Imports"
    },
    {
      "package": "digest",
      "version": ">= 0.6.21",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 0.7.6",
      "role": "Imports"
    },
    {
      "package": "ggforce",
      "version": ">= 0.3.0",
      "role": "Imports"
    },
    {
      "package": "ggiraph",
      "version": ">= 0.5.0",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.0.0",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "version": ">= 0.8.0",
      "role": "Imports"
    },
    {
      "package": "grid",
      "version": ">= 3.5.1",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "version": ">= 1.2.2",
      "role": "Imports"
    },
    {
      "package": "lpSolve",
      "version": ">= 5.6.13",
      "role": "Imports"
    },
    {
      "package": "methods",
      "version": ">= 3.5.0",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "version": ">= 0.2.5",
      "role": "Imports"
    },
    {
      "package": "readr",
      "version": ">= 1.1.1",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "version": ">= 0.2.2",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "version": ">= 1.1.0",
      "role": "Imports"
    },
    {
      "package": "shinycssloaders",
      "version": ">= 0.2.0",
      "role": "Imports"
    },
    {
      "package": "shinyjs",
      "version": ">= 1.0",
      "role": "Imports"
    },
    {
      "package": "shinyWidgets",
      "version": ">= 0.4.8",
      "role": "Imports"
    },
    {
      "package": "stats",
      "version": ">= 3.6.0",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "version": ">= 1.10.1",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "version": ">= 1.4.2",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "version": ">= 0.8.1",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "version": ">= 0.2.4",
      "role": "Imports"
    },
    {
      "package": "tools",
      "version": ">= 3.6.0",
      "role": "Imports"
    },
    {
      "package": "utils",
      "version": ">= 3.5.0",
      "role": "Imports"
    },
    {
      "package": "zeallot",
      "version": ">= 0.1.0",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "version": ">= 2.8.2",
      "role": "Suggests"
    },
    {
      "package": "jpeg",
      "version": ">= 0.1-8",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "version": ">= 1.20",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "version": ">= 1.10",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 2.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.29.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.28.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "transcriptomics",
    "clustering",
    "rnaseq",
    "software"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 416,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SpatialCPie"
  },
  "_mentions": 2,
  "_searchresults": 2,
  "_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/SpatialCPie.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "parseSpotFile",
    "runCPie"
  ],
  "_help": [
    {
      "page": "SpatialCPie-package",
      "title": "SpatialCPie: Cluster analysis of Spatial Transcriptomics data",
      "topics": [
        "SpatialCPie-package",
        "SpatialCPie"
      ]
    },
    {
      "page": "parseSpotFile",
      "title": "Parse spot detector output",
      "topics": [
        "parseSpotFile"
      ]
    },
    {
      "page": "runCPie",
      "title": "Run SpatialCPie",
      "topics": [
        "runCPie"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SpatialCPie/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "bit",
    "bit64",
    "bslib",
    "cachem",
    "cli",
    "clipr",
    "colorspace",
    "commonmark",
    "cpp11",
    "crayon",
    "data.table",
    "DelayedArray",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "fs",
    "gdtools",
    "generics",
    "GenomicRanges",
    "ggforce",
    "ggiraph",
    "ggplot2",
    "ggrepel",
    "glue",
    "gtable",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "igraph",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lifecycle",
    "lpSolve",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "otel",
    "pillar",
    "pkgconfig",
    "polyclip",
    "prettyunits",
    "progress",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "rlang",
    "rmarkdown",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shiny",
    "shinycssloaders",
    "shinyjs",
    "shinyWidgets",
    "sourcetools",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "systemfonts",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tweenr",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml",
    "zeallot"
  ],
  "_vignettes": [
    {
      "source": "SpatialCPie.Rmd",
      "filename": "SpatialCPie.html",
      "title": "Spatial transcriptomics cluster analysis with SpatialCPie",
      "author": "Joseph Bergenstråhle, Ludvig Bergenstråhle, Joakim Lundeberg",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Notice to users using OSX with R-devel",
        "Introduction",
        "Usage example",
        "Input data",
        "Preprocessing",
        "Computing cluster assignments",
        "Visualization",
        "Cluster plot",
        "Spatial array plots",
        "Spot-based clustering",
        "Gene-based clustering",
        "The score multiplier",
        "Sub-clustering"
      ],
      "created": "2018-08-17 15:13:50",
      "modified": "2020-03-31 18:18:55",
      "commits": 41
    }
  ],
  "_score": 4.301029995663981,
  "_indexed": false,
  "_nocasepkg": "spatialcpie",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/SpatialCPie",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-05-30T11:08:08.000Z",
      "distro": "noble",
      "commit": "0234b14f0bd2a4a9c44b522a893184c29088fc90",
      "fileid": "0fd0fb639737ac367b02ef0144993efbf99e87fc2897bc91c098992bb143471d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680861812"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-05-30T11:09:05.000Z",
      "distro": "noble",
      "commit": "0234b14f0bd2a4a9c44b522a893184c29088fc90",
      "fileid": "6917880a3f5ce60ec621171868bdcb073ddeaf1b0d9d8d8de20c4ca7568ea070",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680861812"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-05-30T15:54:00.000Z",
      "commit": "0234b14f0bd2a4a9c44b522a893184c29088fc90",
      "fileid": "5b7f5137d4cdddc883d4ddc871e98ea6b1bdef33158b4bf96e16d8a4a363bcfc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680861812"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-05-30T15:53:53.000Z",
      "commit": "0234b14f0bd2a4a9c44b522a893184c29088fc90",
      "fileid": "54d58f9687431cea8e3018701260e701566e5789e0184487cf6abf127cc41540",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680861812"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.28.0",
      "date": "2026-05-30T11:07:56.000Z",
      "commit": "0234b14f0bd2a4a9c44b522a893184c29088fc90",
      "fileid": "164f2d372337c7100767d084f72d947a317763973c8f024f5d99c70d13dd7f16",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680861812"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-05-30T11:12:20.000Z",
      "commit": "0234b14f0bd2a4a9c44b522a893184c29088fc90",
      "fileid": "9cde40cfee386af915ff881773a3185f5235169c6961b486c1ca1d7a8efac2f7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680861812"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-05-30T11:12:23.000Z",
      "commit": "0234b14f0bd2a4a9c44b522a893184c29088fc90",
      "fileid": "a4baeb2e614a864a3748c4eac846c0a0cd90364c0823221168213b70842a3e00",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680861812"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-05-30T11:06:42.000Z",
      "commit": "0234b14f0bd2a4a9c44b522a893184c29088fc90",
      "fileid": "5017050d63debcfa884d1d0fc97c3aabe51f69f16adb8b01e48dfe28cdd440bd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680861812"
    }
  ]
}