{
  "_id": "6aaafb9e3d719c1f8406a777",
  "Package": "sclValid",
  "Title": "Ensemble Validation and Ranking of Clustering Methods",
  "Version": "0.1.1",
  "Authors@R": "c(\nperson(\ngiven = \"Owen\",\nfamily = \"Visser\",\nrole = c(\"aut\", \"cre\"),\nemail = \"owviss@gmail.com\"\n),\nperson(\ngiven = \"Somnath\",\nfamily = \"Datta\",\nrole = c(\"aut\", \"ctb\")\n),\nperson(\ngiven = \"Justina\",\nfamily = \"Žurauskienė\",\nrole = \"ctb\",\ncomment = \"pcaReduce compatibility code adapted from the pcaReduce package\"\n),\nperson(\ngiven = \"Christopher\",\nfamily = \"Yau\",\nrole = \"ctb\",\ncomment = \"pcaReduce compatibility code adapted from the pcaReduce package\"\n)\n)",
  "Description": "Provides methods for evaluating and comparing clustering\nresults, with an emphasis on sample-level clustering where\nobservations are treated as the units being clustered and\nperturbation is performed by removing samples. The package\nimplements internal, stability, and external validation\nmeasures and supports the comparison and ranking of clustering\nprocedures across tuning parameter choices. It is conceptually\nrelated to the 'clValid' package, which assesses clustering\nstability by perturbing features; in contrast, this package\nfocuses on perturbing the samples being clustered, making the\nvalidation framework suitable for applications such as\nsingle-cell clustering where samples or cells are the primary\nunits of interest. Methods are based in part on Visser and\nDatta (2025) <doi:10.1002/sim.70331>.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "Config/roxygen2/version": "8.1.0",
  "LazyData": "true",
  "Config/pak/sysreqs": "libglpk-dev libpng-dev libxml2-dev libssl-dev\npython3 zlib1g-dev",
  "Repository": "https://owenvisser.r-universe.dev",
  "Date/Publication": "2026-09-16 17:52:56 UTC",
  "RemoteUrl": "https://github.com/owenvisser/sclvalid",
  "RemoteRef": "HEAD",
  "RemoteSha": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-09-16 20:20:40 UTC",
    "User": "root"
  },
  "Author": "Owen Visser [aut, cre],\nSomnath Datta [aut, ctb],\nJustina Žurauskienė [ctb] (pcaReduce compatibility code adapted from\nthe pcaReduce package),\nChristopher Yau [ctb] (pcaReduce compatibility code adapted from the\npcaReduce package)",
  "Maintainer": "Owen Visser <owviss@gmail.com>",
  "_user": "owenvisser",
  "_type": "src",
  "_file": "sclValid_0.1.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/d4eae784727dbcf49737256d15ed815ceaeb03bc40d4749f8c97739aab8a59c3",
  "_filesize": 279961,
  "_sha256": "d4eae784727dbcf49737256d15ed815ceaeb03bc40d4749f8c97739aab8a59c3",
  "_expires": "2026-12-25T20:27:08.000Z",
  "_created": "2026-09-16T20:20:40.000Z",
  "_published": "2026-09-16T20:27:10.118Z",
  "_jobs": [
    {
      "job": 104962232626,
      "time": 152,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10467222966"
    },
    {
      "job": 104962232573,
      "time": 180,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10466517863"
    },
    {
      "job": 104962232657,
      "time": 145,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10467621803"
    },
    {
      "job": 104962232694,
      "time": 166,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10467631986"
    },
    {
      "job": 104962232620,
      "time": 115,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10467297734"
    },
    {
      "job": 104962232654,
      "time": 193,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10467432615"
    },
    {
      "job": 104962232581,
      "time": 136,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10467242790"
    },
    {
      "job": 104962232604,
      "time": 330,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10467133722"
    },
    {
      "job": 104960929342,
      "time": 213,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10467666271"
    },
    {
      "job": 104962232431,
      "time": 146,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10467237903"
    },
    {
      "job": 104962232616,
      "time": 211,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10467657061"
    },
    {
      "job": 104962232699,
      "time": 198,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10467293020"
    },
    {
      "job": 104962232656,
      "time": 129,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10467676735"
    },
    {
      "job": 104962232603,
      "time": 204,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10467686733"
    },
    {
      "job": 104962232583,
      "time": 159,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10467118143"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772",
  "_status": "success",
  "_upstream": "https://github.com/owenvisser/sclvalid",
  "_commit": {
    "id": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
    "author": "owenvisser <owviss@gmail.com>",
    "committer": "owenvisser <owviss@gmail.com>",
    "message": "finally update git ignore what the fucking fuck fuck\n",
    "time": 1789581176
  },
  "_maintainer": {
    "name": "Owen Visser",
    "email": "owviss@gmail.com",
    "login": "owenvisser",
    "description": "PhD Student in Biostatistics\n",
    "uuid": 29928411
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "cccd",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "clue",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "mclust",
      "role": "Imports"
    },
    {
      "package": "mnormt",
      "role": "Imports"
    },
    {
      "package": "pcaMethods",
      "role": "Imports"
    },
    {
      "package": "RaceID",
      "role": "Imports"
    },
    {
      "package": "RankAggreg",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "Rtsne",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    }
  ],
  "_owner": "owenvisser",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-30",
      "n": 1
    },
    {
      "week": "2026-35",
      "n": 9
    },
    {
      "week": "2026-36",
      "n": 1
    },
    {
      "week": "2026-38",
      "n": 13
    }
  ],
  "_tags": [],
  "_topics": [
    "clustering",
    "scrna-seq-analysis",
    "validation",
    "cpp"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "owenvisser",
      "count": 28,
      "uuid": 29928411
    }
  ],
  "_userbio": {
    "uuid": 29928411,
    "type": "user",
    "name": "Owen Visser",
    "followers": 2,
    "description": "PhD Student in Biostatistics\r\n"
  },
  "_downloads": {
    "count": 180,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/sclValid"
  },
  "_devurl": "https://github.com/owenvisser/sclvalid",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/sclValid.html"
  ],
  "_homeurl": "https://github.com/owenvisser/sclvalid",
  "_realowner": "owenvisser",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2026-09-12"
    }
  ],
  "_exports": [
    "check_input",
    "make_sce",
    "run_custom_clustering",
    "run_pcareduce",
    "run_raceid",
    "run_rank_aggregation",
    "run_reduction_clustering",
    "run_validation",
    "scale_validation",
    "validation_apn",
    "validation_ari",
    "validation_average_distance",
    "validation_average_distance_means",
    "validation_bhi",
    "validation_bsi",
    "validation_connectivity",
    "validation_dunn",
    "validation_igp",
    "validation_silhouette"
  ],
  "_datasets": [
    {
      "name": "example_data",
      "title": "Example Single-Cell Expression Data",
      "object": "example_data",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_labels",
      "title": "Example Cell Labels",
      "object": "example_labels",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "check_input",
      "title": "Check Input Data",
      "topics": [
        "check_input"
      ]
    },
    {
      "page": "example_data",
      "title": "Example Single-Cell Expression Data",
      "topics": [
        "example_data"
      ]
    },
    {
      "page": "example_labels",
      "title": "Example Cell Labels",
      "topics": [
        "example_labels"
      ]
    },
    {
      "page": "make_sce",
      "title": "Create a SingleCellExperiment Object",
      "topics": [
        "make_sce"
      ]
    },
    {
      "page": "run_custom_clustering",
      "title": "Run a User-Defined Clustering Method",
      "topics": [
        "run_custom_clustering"
      ]
    },
    {
      "page": "run_pcareduce",
      "title": "Run pcaReduce Clustering",
      "topics": [
        "run_pcareduce"
      ]
    },
    {
      "page": "run_raceid",
      "title": "Run RaceID Clustering",
      "topics": [
        "run_raceid"
      ]
    },
    {
      "page": "run_rank_aggregation",
      "title": "Rank Clustering Solutions",
      "topics": [
        "run_rank_aggregation"
      ]
    },
    {
      "page": "run_reduction_clustering",
      "title": "Run Clustering on PCA and t-SNE Representations",
      "topics": [
        "run_reduction_clustering"
      ]
    },
    {
      "page": "run_validation",
      "title": "Calculate Clustering Validation Measures",
      "topics": [
        "run_validation"
      ]
    },
    {
      "page": "scale_validation",
      "title": "Scale Clustering Validation Measures",
      "topics": [
        "scale_validation"
      ]
    },
    {
      "page": "validation_apn",
      "title": "Calculate Average Proportion of Non-Overlap",
      "topics": [
        "validation_apn"
      ]
    },
    {
      "page": "validation_ari",
      "title": "Calculate Adjusted Rand Index",
      "topics": [
        "validation_ari"
      ]
    },
    {
      "page": "validation_average_distance",
      "title": "Calculate Average Distance",
      "topics": [
        "validation_average_distance"
      ]
    },
    {
      "page": "validation_average_distance_means",
      "title": "Calculate Average Distance Between Means",
      "topics": [
        "validation_average_distance_means"
      ]
    },
    {
      "page": "validation_bhi",
      "title": "Calculate Biological Homogeneity Index",
      "topics": [
        "validation_bhi"
      ]
    },
    {
      "page": "validation_bsi",
      "title": "Calculate Biological Stability Index",
      "topics": [
        "validation_bsi"
      ]
    },
    {
      "page": "validation_connectivity",
      "title": "Calculate Connectivity",
      "topics": [
        "validation_connectivity"
      ]
    },
    {
      "page": "validation_dunn",
      "title": "Calculate the Dunn Index",
      "topics": [
        "validation_dunn"
      ]
    },
    {
      "page": "validation_igp",
      "title": "Calculate In-Group Proportion",
      "topics": [
        "validation_igp"
      ]
    },
    {
      "page": "validation_silhouette",
      "title": "Calculate Average Silhouette Width",
      "topics": [
        "validation_silhouette"
      ]
    }
  ],
  "_readme": "https://github.com/owenvisser/sclvalid/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "Biobase",
    "BiocGenerics",
    "cccd",
    "class",
    "cli",
    "clue",
    "cluster",
    "coop",
    "cowplot",
    "cpp11",
    "DelayedArray",
    "deldir",
    "DEoptimR",
    "diptest",
    "dplyr",
    "farver",
    "FateID",
    "flexmix",
    "FNN",
    "fpc",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "gtools",
    "harmony",
    "here",
    "ica",
    "igraph",
    "IRanges",
    "irlba",
    "isoband",
    "jsonlite",
    "kernlab",
    "labeling",
    "lattice",
    "leiden",
    "lifecycle",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mclust",
    "mgcv",
    "mnormt",
    "modeltools",
    "nlme",
    "nnet",
    "openssl",
    "pcaMethods",
    "permute",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "png",
    "prabclus",
    "princurve",
    "proxy",
    "quadprog",
    "R6",
    "RaceID",
    "randomForest",
    "RankAggreg",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppProgress",
    "RcppTOML",
    "reticulate",
    "RhpcBLASctl",
    "rlang",
    "robustbase",
    "rprojroot",
    "RSpectra",
    "Rtsne",
    "runner",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SingleCellExperiment",
    "som",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyselect",
    "umap",
    "utf8",
    "vctrs",
    "vegan",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "sclvalid",
  "_universes": [
    "owenvisser"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-09-16T20:23:06.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/b6641d46b8e612ee2131da57b1c267804be1163bfb6896c31ee7da27b4f18846",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-09-16T20:23:24.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/0278c04543dce89fd6c61603c41c6286fc24a97851f8413caeaf2606544ff3fb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-09-16T20:23:04.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/44bfe54268eb560d5026812bc533076488a3555aa3c296b86effc57bdd1e31bc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-09-16T20:23:16.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/cd842c2d479dc814c134ad4f01274e9fec2fbc9d74d1962d15de7b73a08f5820",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-09-16T20:22:37.000Z",
      "arch": "aarch64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/60245045086cdfd1938353b7c7520e607dff43b4d229c8912a01c8591776214a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-09-16T20:23:20.000Z",
      "arch": "x86_64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/cf23086508b31a7cdb33e08570f3c23837d461cb52e9eb7bb0389e077a7dc70f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-09-16T20:23:01.000Z",
      "arch": "aarch64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/5df132456956ef87d87076b86e9cca08f8a47cbe3da3734e4c87d21e83e54286",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-09-16T20:23:42.000Z",
      "arch": "x86_64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/0968d0f1726e9b417a2c0a5e643b72e0c733ff44cda34f2f71fa051f035b684f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.1",
      "date": "2026-09-16T20:23:26.000Z",
      "arch": "emscripten",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/a9d722d0d89e78253c27f634ca6c946f09bffa58585517109910260dcda7771a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-09-16T20:23:52.000Z",
      "arch": "aarch64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/9563208564f2f81c1e1a8fde07c87a9b0e49248583b32c14a4b47466de5af35a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-09-16T20:22:35.000Z",
      "arch": "x86_64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/ff19a0a0752103b1f7dd031a66180c693ed4bc73460d39a92682b2a1e0485315",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-09-16T20:22:09.000Z",
      "arch": "x86_64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/8aedd84f58a17ee67af7c035887c292e5ff3968ad467d3794c1238f7bc1f82b8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-09-16T20:23:44.000Z",
      "arch": "aarch64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/d100700c3ef8c8d9f5d8d594e7dc062a9e0207293c63a9da70ea3a3a30353dfd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-09-16T20:22:33.000Z",
      "arch": "x86_64",
      "commit": "f3478141981c25cc28e8ce3e0e67c13485ee57d3",
      "fileid": "https://r2.ropensci.org/24c010e179169d1bc4386bc7fde8de76903f3a9da63148730306cc0d0f951305",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/owenvisser/actions/runs/35145646772"
    }
  ]
}