{
  "_id": "6a1b025d1d7bb097a0a00d2f",
  "Package": "SC3",
  "Type": "Package",
  "Title": "Single-Cell Consensus Clustering",
  "Version": "1.41.0",
  "Author": "Vladimir Kiselev",
  "Maintainer": "Vladimir Kiselev <vladimir.yu.kiselev@gmail.com>",
  "Authors@R": "c(person(\"Vladimir\", \"Kiselev\",\nemail = \"vladimir.yu.kiselev@gmail.com\",\nrole=c(\"cre\", \"aut\")),\nperson(\"Andrew\", \"Yiu\",\nrole=c(\"ctb\")),\nperson(\"Tallulah\", \"Andrews\",\nrole=c(\"ctb\")),\nperson(\"Martin\", \"Hemberg\",\nrole=c(\"aut\")))",
  "Description": "A tool for unsupervised clustering and analysis of single\ncell RNA-Seq data.",
  "License": "GPL-3",
  "LazyData": "TRUE",
  "RoxygenNote": "6.0.1",
  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, SingleCell, Software, Classification,\nClustering, DimensionReduction, SupportVectorMachine, RNASeq,\nVisualization, Transcriptomics, DataRepresentation, GUI,\nDifferentialExpression, Transcription",
  "NeedsCompilation": "yes",
  "URL": "https://github.com/hemberg-lab/SC3",
  "BugReports": "https://support.bioconductor.org/t/sc3/",
  "Config/pak/sysreqs": "cmake make libuv1-dev perl zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:28 UTC",
  "RemoteUrl": "https://github.com/bioc/SC3",
  "RemoteRef": "HEAD",
  "RemoteSha": "05b84c47dae761180996d085f5c519d14c2034cf",
  "Packaged": {
    "Date": "2026-05-30 09:57:30 UTC",
    "User": "root"
  },
  "MD5sum": "501620c7cdda4a43c63e5d6f81935341",
  "_user": "bioc",
  "_type": "src",
  "_file": "SC3_1.41.0.tar.gz",
  "_fileid": "08340ffd01ca2a63bdf824c1d2e24f5e2cf4d9dc75bcdf3bf0c44d494bfdcb63",
  "_filesize": 3527815,
  "_sha256": "08340ffd01ca2a63bdf824c1d2e24f5e2cf4d9dc75bcdf3bf0c44d494bfdcb63",
  "_created": "2026-05-30T09:57:30.000Z",
  "_published": "2026-05-30T15:29:33.669Z",
  "_jobs": [
    {
      "job": 78641161752,
      "time": 209,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307613808"
    },
    {
      "job": 78641161761,
      "time": 283,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307381078"
    },
    {
      "job": 78641161763,
      "time": 368,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307629275"
    },
    {
      "job": 78641161760,
      "time": 263,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307379211"
    },
    {
      "job": 78641161759,
      "time": 350,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307627610"
    },
    {
      "job": 78641161796,
      "time": 193,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7309249072"
    },
    {
      "job": 78641161792,
      "time": 502,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307531969"
    },
    {
      "job": 78641161794,
      "time": 234,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7309252076"
    },
    {
      "job": 78641161784,
      "time": 458,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307528232"
    },
    {
      "job": 78639982759,
      "time": 703,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307353847"
    },
    {
      "job": 78641161747,
      "time": 169,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307609567"
    },
    {
      "job": 78641161791,
      "time": 291,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307621175"
    },
    {
      "job": 78641161758,
      "time": 273,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307619349"
    },
    {
      "job": 78641161762,
      "time": 258,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307617759"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 4,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SC3",
  "_commit": {
    "id": "05b84c47dae761180996d085f5c519d14c2034cf",
    "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": 1777380148
  },
  "_maintainer": {
    "name": "Vladimir Kiselev",
    "email": "vladimir.yu.kiselev@gmail.com",
    "login": "wikiselev",
    "description": "Building Scalable Bioinformatics & AI Solutions | Cloud Infrastructure, Pipelines & Data Science Expert, Single-Cell, Drug Discovery",
    "uuid": 2342606
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "e1071",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "doRNG",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "version": ">= 1.0.8",
      "role": "Imports"
    },
    {
      "package": "ROCR",
      "role": "Imports"
    },
    {
      "package": "robustbase",
      "role": "Imports"
    },
    {
      "package": "rrcov",
      "role": "Imports"
    },
    {
      "package": "cluster",
      "role": "Imports"
    },
    {
      "package": "WriteXLS",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.11.1",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "mclust",
      "role": "Suggests"
    },
    {
      "package": "scater",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "singlecell",
    "software",
    "classification",
    "clustering",
    "dimensionreduction",
    "supportvectormachine",
    "rnaseq",
    "visualization",
    "transcriptomics",
    "datarepresentation",
    "gui",
    "differentialexpression",
    "transcription",
    "bioconductor-package",
    "human-cell-atlas",
    "single-cell-rna-seq",
    "openblas",
    "cpp"
  ],
  "_stars": 129,
  "_contributors": [
    {
      "user": "wikiselev",
      "count": 267,
      "uuid": 2342606
    },
    {
      "user": "dtenenba",
      "count": 7,
      "uuid": 2286826
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    },
    {
      "user": "nh3",
      "count": 3,
      "uuid": 421523
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "shians",
      "count": 2,
      "uuid": 6036662
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "kayla-morrell",
      "count": 1,
      "uuid": 32339524
    },
    {
      "user": "pati-ni",
      "count": 1,
      "uuid": 14965608
    },
    {
      "user": "tallulandrews",
      "count": 1,
      "uuid": 13570376
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 846,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SC3"
  },
  "_mentions": 71,
  "_devurl": "https://github.com/hemberg-lab/sc3",
  "_searchresults": 394,
  "_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/SC3.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/hemberg-lab/sc3",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "consensus_matrix",
    "get_de_genes",
    "get_marker_genes",
    "get_outl_cells",
    "get_processed_dataset",
    "norm_laplacian",
    "reindex_clusters",
    "sc3",
    "sc3_calc_biology",
    "sc3_calc_consens",
    "sc3_calc_dists",
    "sc3_calc_transfs",
    "sc3_estimate_k",
    "sc3_export_results_xls",
    "sc3_interactive",
    "sc3_kmeans",
    "sc3_plot_cluster_stability",
    "sc3_plot_consensus",
    "sc3_plot_de_genes",
    "sc3_plot_expression",
    "sc3_plot_markers",
    "sc3_plot_silhouette",
    "sc3_prepare",
    "sc3_run_svm"
  ],
  "_datasets": [
    {
      "name": "ann",
      "title": "Cell type annotations for data extracted from a publication by Yan et al.",
      "object": "yan",
      "class": [
        "data.frame"
      ],
      "fields": [
        "cell_type1"
      ],
      "rows": 90,
      "table": true,
      "tojson": true
    },
    {
      "name": "yan",
      "title": "Single cell RNA-Seq data extracted from a publication by Yan et al.",
      "object": "yan",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Oocyte..1.RPKM.",
        "Oocyte..2.RPKM.",
        "Oocyte..3.RPKM.",
        "Zygote..1.RPKM.",
        "Zygote..2.RPKM.",
        "Zygote..3.RPKM.",
        "X2.cell.embryo.1..Cell.1.RPKM.",
        "X2.cell.embryo.1..Cell.2.RPKM.",
        "X2.cell.embryo.2..Cell.1.RPKM.",
        "X2.cell.embryo.2..Cell.2.RPKM.",
        "X2.cell.embryo.3..Cell.1.RPKM.",
        "X2.cell.embryo.3..Cell.2.RPKM.",
        "X4.cell.embryo.1..Cell.1.RPKM.",
        "X4.cell.embryo.1..Cell.2.RPKM.",
        "X4.cell.embryo.1..Cell.3.RPKM.",
        "X4.cell.embryo.1..Cell.4.RPKM.",
        "X4.cell.embryo.2..Cell.1.RPKM.",
        "X4.cell.embryo.2..Cell.2.RPKM.",
        "X4.cell.embryo.2..Cell.3.RPKM.",
        "X4.cell.embryo.2..Cell.4.RPKM.",
        "X4.cell.embryo.3..Cell.1.RPKM.",
        "X4.cell.embryo.3..Cell.2.RPKM.",
        "X4.cell.embryo.3..Cell.3.RPKM.",
        "X4.cell.embryo.3..Cell.4.RPKM.",
        "X8.cell.embryo.1..Cell.1.RPKM.",
        "X8.cell.embryo.1..Cell.2.RPKM.",
        "X8.cell.embryo.1..Cell.3.RPKM.",
        "X8.cell.embryo.1..Cell.4.RPKM.",
        "X8.cell.embryo.2..Cell.1.RPKM.",
        "X8.cell.embryo.2..Cell.2.RPKM.",
        "X8.cell.embryo.2..Cell.3.RPKM.",
        "X8.cell.embryo.2..Cell.4.RPKM.",
        "X8.cell.embryo.2..Cell.5.RPKM.",
        "X8.cell.embryo.2..Cell.6.RPKM.",
        "X8.cell.embryo.2..Cell.7.RPKM.",
        "X8.cell.embryo.2..Cell.8.RPKM.",
        "X8.cell.embryo.3..Cell.1.RPKM.",
        "X8.cell.embryo.3..Cell.2.RPKM.",
        "X8.cell.embryo.3..Cell.3.RPKM.",
        "X8.cell.embryo.3..Cell.4.RPKM.",
        "X8.cell.embryo.3..Cell.5.RPKM.",
        "X8.cell.embryo.3..Cell.6.RPKM.",
        "X8.cell.embryo.3..Cell.7.RPKM.",
        "X8.cell.embryo.3..Cell.8.RPKM.",
        "Morulae..1..Cell.1.RPKM.",
        "Morulae..1..Cell.2.RPKM.",
        "Morulae..1..Cell.3.RPKM.",
        "Morulae..1..Cell.4.RPKM.",
        "Morulae..1..Cell.5.RPKM.",
        "Morulae..1..Cell.6.RPKM.",
        "Morulae..1..Cell.7.RPKM.",
        "Morulae..1..Cell.8.RPKM.",
        "Morulae..2..Cell.1.RPKM.",
        "Morulae..2..Cell.2.RPKM.",
        "Morulae..2..Cell.3.RPKM.",
        "Morulae..2..Cell.4.RPKM.",
        "Morulae..2..Cell.5.RPKM.",
        "Morulae..2..Cell.6.RPKM.",
        "Morulae..2..Cell.7.RPKM.",
        "Morulae..2..Cell.8.RPKM.",
        "Late.blastocyst..1..Cell.1.RPKM.",
        "Late.blastocyst..1..Cell.2.RPKM.",
        "Late.blastocyst..1..Cell.3.RPKM.",
        "Late.blastocyst..1..Cell.4.RPKM.",
        "Late.blastocyst..1..Cell.5.RPKM.",
        "Late.blastocyst..1..Cell.6.RPKM.",
        "Late.blastocyst..1..Cell.7.RPKM.",
        "Late.blastocyst..1..Cell.8.RPKM.",
        "Late.blastocyst..1..Cell.9.RPKM.",
        "Late.blastocyst..1..Cell.10.RPKM.",
        "Late.blastocyst..1..Cell.11.RPKM.",
        "Late.blastocyst..1..Cell.12.RPKM.",
        "Late.blastocyst..2..Cell.1.RPKM.",
        "Late.blastocyst..2..Cell.2.RPKM.",
        "Late.blastocyst..2..Cell.3.RPKM.",
        "Late.blastocyst..2..Cell.4.RPKM.",
        "Late.blastocyst..2..Cell.5.RPKM.",
        "Late.blastocyst..2..Cell.6.RPKM.",
        "Late.blastocyst..2..Cell.7.RPKM.",
        "Late.blastocyst..2..Cell.8.RPKM.",
        "Late.blastocyst..2..Cell.9.RPKM.",
        "Late.blastocyst..2..Cell.10.RPKM.",
        "Late.blastocyst..3..Cell.1.RPKM.",
        "Late.blastocyst..3..Cell.2.RPKM.",
        "Late.blastocyst..3..Cell.3.RPKM.",
        "Late.blastocyst..3..Cell.4.RPKM.",
        "Late.blastocyst..3..Cell.5.RPKM.",
        "Late.blastocyst..3..Cell.6.RPKM.",
        "Late.blastocyst..3..Cell.7.RPKM.",
        "Late.blastocyst..3..Cell.8.RPKM."
      ],
      "rows": 20214,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ann",
      "title": "Cell type annotations for data extracted from a publication by Yan et al.",
      "topics": [
        "ann"
      ]
    },
    {
      "page": "calculate_distance",
      "title": "Calculate a distance matrix",
      "topics": [
        "calculate_distance"
      ]
    },
    {
      "page": "calculate_stability",
      "title": "Calculate the stability index of the obtained clusters when changing 'k'",
      "topics": [
        "calculate_stability"
      ]
    },
    {
      "page": "consensus_matrix",
      "title": "Calculate consensus matrix",
      "topics": [
        "consensus_matrix"
      ]
    },
    {
      "page": "consmx",
      "title": "Consensus matrix computation",
      "topics": [
        "consmx"
      ]
    },
    {
      "page": "ED1",
      "title": "Compute Euclidean distance matrix by rows",
      "topics": [
        "ED1"
      ]
    },
    {
      "page": "ED2",
      "title": "Compute Euclidean distance matrix by columns",
      "topics": [
        "ED2"
      ]
    },
    {
      "page": "estkTW",
      "title": "Estimate the optimal k for k-means clustering",
      "topics": [
        "estkTW"
      ]
    },
    {
      "page": "get_auroc",
      "title": "Calculate the area under the ROC curve for a given gene.",
      "topics": [
        "get_auroc"
      ]
    },
    {
      "page": "get_biolgy",
      "title": "Wrapper for calculating biological properties",
      "topics": [
        "get_biolgy"
      ]
    },
    {
      "page": "get_de_genes",
      "title": "Find differentially expressed genes",
      "topics": [
        "get_de_genes"
      ]
    },
    {
      "page": "get_marker_genes",
      "title": "Calculate marker genes",
      "topics": [
        "get_marker_genes"
      ]
    },
    {
      "page": "get_outl_cells",
      "title": "Find cell outliers in each cluster.",
      "topics": [
        "get_outl_cells"
      ]
    },
    {
      "page": "get_processed_dataset",
      "title": "Get processed dataset used by 'SC3' clustering",
      "topics": [
        "get_processed_dataset"
      ]
    },
    {
      "page": "markers_for_heatmap",
      "title": "Reorder and subset gene markers for plotting on a heatmap",
      "topics": [
        "markers_for_heatmap"
      ]
    },
    {
      "page": "norm_laplacian",
      "title": "Graph Laplacian calculation",
      "topics": [
        "norm_laplacian"
      ]
    },
    {
      "page": "organise_de_genes",
      "title": "Get differentiall expressed genes from an object of 'SingleCellExperiment' class",
      "topics": [
        "organise_de_genes"
      ]
    },
    {
      "page": "organise_marker_genes",
      "title": "Get marker genes from an object of 'SingleCellExperiment' class",
      "topics": [
        "organise_marker_genes"
      ]
    },
    {
      "page": "prepare_for_svm",
      "title": "A helper function for the SVM analysis",
      "topics": [
        "prepare_for_svm"
      ]
    },
    {
      "page": "reindex_clusters",
      "title": "Reindex cluster labels in ascending order",
      "topics": [
        "reindex_clusters"
      ]
    },
    {
      "page": "sc3",
      "title": "Run all steps of 'SC3' in one go",
      "topics": [
        "sc3",
        "sc3,SingleCellExperiment-method",
        "sc3.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_calc_biology",
      "title": "Calculate DE genes, marker genes and cell outliers.",
      "topics": [
        "sc3_calc_biology",
        "sc3_calc_biology,",
        "sc3_calc_biology,SingleCellExperiment-method",
        "sc3_calc_biology.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_calc_consens",
      "title": "Calculate consensus matrix.",
      "topics": [
        "sc3_calc_consens",
        "sc3_calc_consens,",
        "sc3_calc_consens,SingleCellExperiment-method",
        "sc3_calc_consens.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_calc_dists",
      "title": "Calculate distances between the cells.",
      "topics": [
        "sc3_calc_dists",
        "sc3_calc_dists,",
        "sc3_calc_dists,SingleCellExperiment-method",
        "sc3_calc_dists.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_calc_transfs",
      "title": "Calculate transformations of the distance matrices.",
      "topics": [
        "sc3_calc_transfs",
        "sc3_calc_transfs,",
        "sc3_calc_transfs,SingleCellExperiment-method",
        "sc3_calc_transfs.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_estimate_k",
      "title": "Estimate the optimal number of cluster 'k' for a scRNA-Seq expression matrix",
      "topics": [
        "sc3_estimate_k",
        "sc3_estimate_k,SingleCellExperiment-method",
        "sc3_estimate_k.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_export_results_xls",
      "title": "Write 'SC3' results to Excel file",
      "topics": [
        "sc3_export_results_xls",
        "sc3_export_results_xls,SingleCellExperiment-method",
        "sc3_export_results_xls.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_interactive",
      "title": "Opens 'SC3' results in an interactive session in a web browser.",
      "topics": [
        "sc3_interactive",
        "sc3_interactive,",
        "sc3_interactive,SingleCellExperiment-method",
        "sc3_interactive.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_kmeans",
      "title": "'kmeans' clustering of cells.",
      "topics": [
        "sc3_kmeans",
        "sc3_kmeans,",
        "sc3_kmeans,SingleCellExperiment-method",
        "sc3_kmeans.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_plot_cluster_stability",
      "title": "Plot stability of the clusters",
      "topics": [
        "sc3_plot_cluster_stability",
        "sc3_plot_cluster_stability,",
        "sc3_plot_cluster_stability,SingleCellExperiment-method",
        "sc3_plot_cluster_stability.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_plot_consensus",
      "title": "Plot consensus matrix as a heatmap",
      "topics": [
        "sc3_plot_consensus",
        "sc3_plot_consensus,",
        "sc3_plot_consensus,SingleCellExperiment-method",
        "sc3_plot_consensus.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_plot_de_genes",
      "title": "Plot expression of DE genes of the clusters identified by 'SC3' as a heatmap",
      "topics": [
        "sc3_plot_de_genes",
        "sc3_plot_de_genes,",
        "sc3_plot_de_genes,SingleCellExperiment-method",
        "sc3_plot_de_genes.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_plot_expression",
      "title": "Plot expression matrix used for SC3 clustering as a heatmap",
      "topics": [
        "sc3_plot_expression",
        "sc3_plot_expression,",
        "sc3_plot_expression,SingleCellExperiment-method",
        "sc3_plot_expression.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_plot_markers",
      "title": "Plot expression of marker genes identified by 'SC3' as a heatmap.",
      "topics": [
        "sc3_plot_markers",
        "sc3_plot_markers,",
        "sc3_plot_markers,SingleCellExperiment-method",
        "sc3_plot_markers.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_plot_silhouette",
      "title": "Plot silhouette indexes of the cells",
      "topics": [
        "sc3_plot_silhouette",
        "sc3_plot_silhouette,",
        "sc3_plot_silhouette,SingleCellExperiment-method",
        "sc3_plot_silhouette.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_prepare",
      "title": "Prepare the 'SingleCellExperiment' object for 'SC3' clustering.",
      "topics": [
        "sc3_prepare",
        "sc3_prepare,SingleCellExperiment-method",
        "sc3_prepare.SingleCellExperiment"
      ]
    },
    {
      "page": "sc3_run_svm",
      "title": "Run the hybrid 'SVM' approach.",
      "topics": [
        "sc3_run_svm",
        "sc3_run_svm,",
        "sc3_run_svm,SingleCellExperiment-method",
        "sc3_run_svm.SingleCellExperiment"
      ]
    },
    {
      "page": "support_vector_machines",
      "title": "Run support vector machines ('SVM') prediction",
      "topics": [
        "support_vector_machines"
      ]
    },
    {
      "page": "tmult",
      "title": "Matrix left-multiplied by its transpose",
      "topics": [
        "tmult"
      ]
    },
    {
      "page": "transformation",
      "title": "Distance matrix transformation",
      "topics": [
        "transformation"
      ]
    },
    {
      "page": "yan",
      "title": "Single cell RNA-Seq data extracted from a publication by Yan et al.",
      "topics": [
        "yan"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SC3/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "bitops",
    "bslib",
    "cachem",
    "caTools",
    "class",
    "cli",
    "cluster",
    "codetools",
    "commonmark",
    "cpp11",
    "DelayedArray",
    "DEoptimR",
    "digest",
    "doParallel",
    "doRNG",
    "e1071",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "fs",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "htmltools",
    "httpuv",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "labeling",
    "later",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "mvtnorm",
    "otel",
    "pcaPP",
    "pheatmap",
    "promises",
    "proxy",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "rngtools",
    "robustbase",
    "ROCR",
    "rrcov",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shiny",
    "SingleCellExperiment",
    "sourcetools",
    "SparseArray",
    "SummarizedExperiment",
    "vctrs",
    "viridisLite",
    "withr",
    "WriteXLS",
    "xtable",
    "XVector"
  ],
  "_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"
    }
  ],
  "_vignettes": [
    {
      "source": "SC3.Rmd",
      "filename": "SC3.html",
      "title": "SC3 package manual",
      "author": "Vladimir Kiselev",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "SingleCellExperiment, QC and scater",
        "Quick Start",
        "SC3 Input",
        "Run SC3",
        "colData",
        "rowData",
        "Number of Сells",
        "Plot Functions",
        "Consensus Matrix",
        "Silhouette Plot",
        "Expression Matrix",
        "Cluster Stability",
        "DE genes",
        "Marker Genes",
        "SC3 in Detail",
        "sc3_prepare",
        "(optional) sc3_estimate_k",
        "sc3_calc_dists",
        "sc3_calc_transfs",
        "sc3_kmeans",
        "sc3_calc_consens",
        "(optional) sc3_calc_biology",
        "Cell Outliers",
        "DE and marker genes",
        "Hybrid SVM Approach"
      ],
      "created": "2017-10-04 20:05:16",
      "modified": "2023-05-15 17:34:22",
      "commits": 12
    }
  ],
  "_score": 10.137449696283811,
  "_indexed": true,
  "_nocasepkg": "sc3",
  "_universes": [
    "bioc",
    "wikiselev",
    "hemberg-lab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-05-30T10:01:07.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "43b13d3a0e18b2daea3a3b825493d66f913d6efb3527abd881da250dc6712536",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-05-30T10:46:05.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "508442d308c6beee0302c92d7bac2a217ecd15a0a9a881af870e6f0b5d65b23c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-05-30T10:00:54.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "84895c80af6086df9ee3005ca64d3042a60f7d0751e6ce8771f444119bc17665",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-05-30T10:45:43.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "1103e471c1933e821f9c2666ee37d28a77cc14f81f9428c598bc569941003c28",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-05-30T15:26:57.000Z",
      "arch": "aarch64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "a9128512acbc8fe0f46183f14b6b7cd93ef68b8a6900498662d1b58d9c1ca084",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-05-30T10:26:32.000Z",
      "arch": "x86_64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "ff8e73fa0033c76e4e6e7df792656ee4ded011fc65e9a33ff098d6fe7820cdfd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-05-30T15:27:10.000Z",
      "arch": "aarch64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "33a47b156d512a2ad9b530733309ca2b037fb842dcf6c6fd899b688d8ab6e809",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-05-30T10:27:16.000Z",
      "arch": "x86_64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "3d40b5259d8953b0dcd03490a3dc7900f68aa27ffcffb7ad65648cee7bc0f5a2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-05-30T10:44:54.000Z",
      "arch": "emscripten",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "1bb43adfa105603acaf80e05650b0875e0c88bdc33b2f3383381316fd4bdf8fb",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-05-30T10:44:19.000Z",
      "arch": "x86_64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "2b99090016051b88af9bc1ad633e440b6ccc802c5f70e8f1ea9b410373c87d32",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-05-30T10:43:44.000Z",
      "arch": "x86_64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "de4d15a64fe263aa591a1b8a0cea4e1c6bc965dd0a12bbc47bdfbe089917103e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-05-30T10:43:32.000Z",
      "arch": "x86_64",
      "commit": "05b84c47dae761180996d085f5c519d14c2034cf",
      "fileid": "41c572fe885247e3592a026b80ca7768c86f61b625762f76c403ca7763645e22",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676985732"
    }
  ]
}