{
  "_id": "6a494df6f6c47c4419499f21",
  "Package": "FuseSOM",
  "Title": "A Correlation Based Multiview Self Organizing Maps Clustering\nFor IMC Datasets",
  "Version": "1.15.0",
  "Authors@R": "person(\"Elijah\", \"Willie\", , \"ewil3501@uni.sydney.edu.au\", role = c(\"aut\", \"cre\"))",
  "Description": "A correlation-based multiview self-organizing map for the\ncharacterization of cell types in highly multiplexed in situ\nimaging cytometry assays (`FuseSOM`) is a tool for unsupervised\nclustering. `FuseSOM` is robust and achieves high accuracy by\ncombining a `Self Organizing Map` architecture and a\n`Multiview` integration of correlation based metrics. This\nallows FuseSOM to cluster highly multiplexed in situ imaging\ncytometry assays.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.2",
  "LazyData": "false",
  "BuildResaveData": "false",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/ecool50/FuseSOM/issues",
  "biocViews": "SingleCell, CellBasedAssays, Clustering, Spatial",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:59:22 UTC",
  "RemoteUrl": "https://github.com/bioc/FuseSOM",
  "RemoteRef": "HEAD",
  "RemoteSha": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-03 22:35:16 UTC",
    "User": "root"
  },
  "Author": "Elijah Willie [aut, cre]",
  "Maintainer": "Elijah Willie <ewil3501@uni.sydney.edu.au>",
  "_user": "bioc",
  "_type": "src",
  "_file": "FuseSOM_1.15.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/6441eadb5a43e4b7b44e99c4ed032d53ab2f3aeaa26afd4a016805c7a837a49b",
  "_filesize": 2692197,
  "_sha256": "6441eadb5a43e4b7b44e99c4ed032d53ab2f3aeaa26afd4a016805c7a837a49b",
  "_expires": "2026-10-12T18:16:20.000Z",
  "_created": "2026-07-03T22:35:16.000Z",
  "_published": "2026-07-04T18:16:22.601Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449",
  "_status": "success",
  "_upstream": "https://github.com/bioc/FuseSOM",
  "_commit": {
    "id": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
    "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": 1777381162
  },
  "_maintainer": {
    "name": "Elijah Willie",
    "email": "ewil3501@uni.sydney.edu.au",
    "login": "ecool50",
    "description": "",
    "uuid": 8261982
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85155480232,
      "time": 202,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8075706071"
    },
    {
      "job": 85155480222,
      "time": 303,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8075721271"
    },
    {
      "job": 85155480284,
      "time": 328,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8075724651"
    },
    {
      "job": 85155480316,
      "time": 248,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8075713194"
    },
    {
      "job": 85155480236,
      "time": 297,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8075719992"
    },
    {
      "job": 85155480507,
      "time": 154,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8075711547"
    },
    {
      "job": 85155480530,
      "time": 345,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8075727276"
    },
    {
      "job": 85155480474,
      "time": 157,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8075699089"
    },
    {
      "job": 85155480510,
      "time": 345,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8075727523"
    },
    {
      "job": 85155480326,
      "time": 297,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8075673816"
    },
    {
      "job": 85155480337,
      "time": 191,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8075704285"
    },
    {
      "job": 85155480245,
      "time": 224,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8075709248"
    },
    {
      "job": 85155480526,
      "time": 243,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8075711981"
    },
    {
      "job": 85155480319,
      "time": 216,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8075707987"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "psych",
      "role": "Imports"
    },
    {
      "package": "FCPS",
      "role": "Imports"
    },
    {
      "package": "analogue",
      "role": "Imports"
    },
    {
      "package": "coop",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "ggplotify",
      "role": "Imports"
    },
    {
      "package": "fastcluster",
      "role": "Imports"
    },
    {
      "package": "fpc",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "proxy",
      "role": "Imports"
    },
    {
      "package": "cluster",
      "role": "Imports"
    },
    {
      "package": "diptest",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.15.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.14.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "singlecell",
    "cellbasedassays",
    "clustering",
    "spatial"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "nick-robo",
      "count": 67,
      "uuid": 17681331
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    },
    {
      "user": "ecool50",
      "count": 2,
      "uuid": 8261982
    },
    {
      "user": "ellispatrick",
      "count": 1,
      "uuid": 8390021
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/ecool50/fusesom",
  "_searchresults": 24,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/FuseSOM.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ecool50/fusesom",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "clusterPrototypes",
    "computeGridSize",
    "estimateNumCluster",
    "generatePrototypes",
    "markerHeatmap",
    "normaliseData",
    "optiPlot",
    "runFuseSOM"
  ],
  "_datasets": [
    {
      "name": "risom_dat",
      "title": "IMC Breast Cancer Data Data from A spatial atlas of breast cancer progression using MIBI-TOF and tissue transcriptomics",
      "object": "risom_dat",
      "file": "risom_dat.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CD45",
        "SMA",
        "CK7",
        "CK5",
        "VIM",
        "CD31",
        "PanKRT",
        "ECAD",
        "Tryptase",
        "MPO",
        "CD20",
        "CD3",
        "CD8",
        "CD4",
        "CD14",
        "CD68",
        "FAP",
        "CD36",
        "CD11c",
        "HLADRDPDQ",
        "P63",
        "CD44",
        "CellType"
      ],
      "rows": 69672,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dot-arsinhNnorm",
      "title": "Function to do arsinh normalization",
      "topics": [
        ".arsinhNnorm"
      ]
    },
    {
      "page": "dot-computeElbow",
      "title": "A function to compute the elbow point given a set of points",
      "topics": [
        ".computeElbow"
      ]
    },
    {
      "page": "dot-minmaxNorm",
      "title": "Function to do min max normalization",
      "topics": [
        ".minmaxNorm"
      ]
    },
    {
      "page": "dot-percentileNorm",
      "title": "Function to do percentile normalizaton",
      "topics": [
        ".percentileNorm"
      ]
    },
    {
      "page": "dot-runDiscriminant",
      "title": "Discriminant cluster estimator",
      "topics": [
        ".runDiscriminant"
      ]
    },
    {
      "page": "dot-uniformData",
      "title": "Creates uniformly distributed data of same dimensionality as input data this function was obtained from the Stab package",
      "topics": [
        ".uniformData"
      ]
    },
    {
      "page": "clusterPrototypes",
      "title": "Cluster prototypes",
      "topics": [
        "clusterPrototypes"
      ]
    },
    {
      "page": "computeGridSize",
      "title": "Estimate the optimal grid size",
      "topics": [
        "computeGridSize"
      ]
    },
    {
      "page": "estimateNumCluster",
      "title": "Estimate number of clusters",
      "topics": [
        "estimateNumCluster"
      ]
    },
    {
      "page": "FuseSOM",
      "title": "FuseSOM",
      "topics": [
        "FuseSOM"
      ]
    },
    {
      "page": "generatePrototypes",
      "title": "Generate a Self Organizing Map",
      "topics": [
        "generatePrototypes"
      ]
    },
    {
      "page": "markerHeatmap",
      "title": "Generate expression heatmap",
      "topics": [
        "markerHeatmap"
      ]
    },
    {
      "page": "normaliseData",
      "title": "Normalise Marker Intensities",
      "topics": [
        "normaliseData"
      ]
    },
    {
      "page": "normalizeData",
      "title": "Normalize Marker Intensities",
      "topics": [
        "normalizeData"
      ]
    },
    {
      "page": "optiPlot",
      "title": "Generate elbow plots",
      "topics": [
        "optiPlot"
      ]
    },
    {
      "page": "risom_dat",
      "title": "IMC Breast Cancer Data Data from A spatial atlas of breast cancer progression using MIBI-TOF and tissue transcriptomics",
      "topics": [
        "diabetesData",
        "risom_dat"
      ]
    },
    {
      "page": "runFuseSOM",
      "title": "A wrapper function to run the FuseSOM algorithm",
      "topics": [
        "runFuseSOM"
      ]
    },
    {
      "page": "somInitPca.default",
      "title": "these functions were obtained from https://rdrr.io/rforge/yasomi/ with some major modifications",
      "topics": [
        "somInitPca.default"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/FuseSOM/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "analogue",
    "backports",
    "Biobase",
    "BiocGenerics",
    "boot",
    "brglm",
    "broom",
    "car",
    "carData",
    "class",
    "cli",
    "cluster",
    "colorspace",
    "coop",
    "corrplot",
    "cowplot",
    "cpp11",
    "DataVisualizations",
    "DelayedArray",
    "DEoptimR",
    "Deriv",
    "digest",
    "diptest",
    "doBy",
    "dplyr",
    "farver",
    "fastcluster",
    "FCPS",
    "flexmix",
    "forecast",
    "Formula",
    "fpc",
    "fracdiff",
    "fs",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggplotify",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "GPArotation",
    "gridExtra",
    "gridGraphics",
    "gtable",
    "IRanges",
    "isoband",
    "kernlab",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "mclust",
    "mgcv",
    "minqa",
    "mnormt",
    "modelr",
    "modeltools",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "pbkrtest",
    "permute",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plyr",
    "polynom",
    "prabclus",
    "pracma",
    "princurve",
    "profileModel",
    "proxy",
    "psych",
    "purrr",
    "quantreg",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppParallel",
    "Rdpack",
    "reformulas",
    "reshape2",
    "rlang",
    "robustbase",
    "rstatix",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "sp",
    "SparseArray",
    "SparseM",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "vctrs",
    "vegan",
    "viridisLite",
    "withr",
    "XVector",
    "yulab.utils",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "Introduction.Rmd",
      "filename": "Introduction.html",
      "title": "FuseSOM package manual",
      "author": "Elijah Willie",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Introduction",
        "Disclaimer",
        "Getting Started",
        "FuseSOM Matrix Input",
        "Using FuseSOM to estimate the number of clusters",
        "FuseSOM Sinlge Cell Epxeriment object as input.",
        "Using FuseSOM to estimate the number of clusters for single cell experiment objects",
        "FuseSOM Spatial Epxeriment object as input.",
        "sessionInfo()"
      ],
      "created": "2022-06-22 21:05:06",
      "modified": "2022-10-05 05:19:48",
      "commits": 15
    }
  ],
  "_score": 4.857332496431269,
  "_indexed": true,
  "_nocasepkg": "fusesom",
  "_universes": [
    "bioc",
    "ecool50"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-07-03T22:39:11.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/79bc03f4f125b242d2934b57055e0e47275feacc71164d2e02d676d199cbf740",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-07-03T22:39:05.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/abdd64621c340315f32066b8a0109ae1edb76728870b6f2b765b3d49412396ea",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-07-03T22:38:28.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/711812d8f63de869e1ae5a014ded0d433d96e0cdb246a33d8c1858b43adbb544",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-07-03T22:38:34.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/3b503a4d1b49bb9a088a32ab6f61e4f67b1d26181180545a10443da245d326a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-07-03T22:38:31.000Z",
      "arch": "aarch64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/1795c6c4421fe00d8c3c26c703758f06cc41dfc76956eda79ff4e8582f4a320b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-07-03T22:38:17.000Z",
      "arch": "x86_64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/1555db2af7e17544e822fb7c162ccc001b6d541c19ec785085917f170c158699",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-07-03T22:37:06.000Z",
      "arch": "aarch64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/0f2328cbbbe34eece67cfb6c4a5255d465ad6482954f96e3f74d5387e6c79f7b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-07-03T22:38:30.000Z",
      "arch": "x86_64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/dd71ad00df1006eb055c42a89a94f2047cb24adc5dd7c536bbc6b7d0853346b3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.15.0",
      "date": "2026-07-03T22:39:00.000Z",
      "arch": "emscripten",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/138be862a31cb49321157e23fdc99f312715ce186b035589dbdb61f22c1a2c82",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-07-03T22:37:02.000Z",
      "arch": "x86_64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/48ffd31a3bf44c387329fe878db947c13e06db52371516aa8b56645367dba027",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-07-03T22:37:07.000Z",
      "arch": "x86_64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/fb12a2f5dc6b2f9808fc8fb0f24b729b5694c7dc60918cd35e2f43baa0557a12",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-07-03T22:37:01.000Z",
      "arch": "x86_64",
      "commit": "e6e84914d8f60031513b6e205c7abb684b9d1aa3",
      "fileid": "https://r2.ropensci.org/0a3cd3d2ebd9dd0ea2256c09e5f4865834706a67614b0a8f3a887cec8006b275",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686094449"
    }
  ]
}