{
  "_id": "6aba665099f7aa8c6aa41237",
  "Package": "ClustAssess",
  "Type": "Package",
  "Title": "Tools for Assessing Clustering",
  "Version": "1.2.0",
  "Authors@R": "c(person(\"Andi\", \"Munteanu\",\nemail=\"am3019@cam.ac.uk\", role=c(\"aut\", \"cre\")), person(\"Arash\", \"Shahsavari\", email=\"arash8579@hotmail.com\",\nrole = c(\"aut\")), person(\"Rafael\", \"Kollyfas\", role=c(\"ctb\"), email=\"rk720@cam.ac.uk\"), person(\"Miguel\", \"Larraz Lopez de Novales\", role=c(\"aut\"), email =\"ml2088@cam.ac.uk\"), person(\"Liviu\", \"Ciortuz\", role=c(\"ctb\"), email=\"liviu_ciortuz@yahoo.co.uk\"), person(\"Irina\", \"Mohorianu\",\nemail=\"iim22@cam.ac.uk\", role=c(\"aut\")))",
  "Description": "A set of tools for evaluating clustering robustness using\nproportion of ambiguously clustered pairs (Senbabaoglu et al.\n(2014) <doi:10.1038/srep06207>), as well as similarity across\nmethods and method stability using element-centric clustering\ncomparison (Gates et al. (2019)\n<doi:10.1038/s41598-019-44892-y>). Additionally, this package\nenables stability-based parameter assessment for graph-based\nclustering pipelines typical in single-cell data analysis.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Additional_repositories": "https://blaserlab.r-universe.dev",
  "biocViews": "Software, SingleCell, RNASeq, ATACSeq, Normalization,\nPreprocessing, DimensionReduction, Visualization,\nQualityControl, Clustering, Classification, Annotation,\nGeneExpression, DifferentialExpression",
  "Roxygen": "list(markdown = TRUE)",
  "URL": "https://github.com/Core-Bioinformatics/ClustAssess,\nhttps://core-bioinformatics.github.io/ClustAssess/",
  "BugReports": "https://github.com/Core-Bioinformatics/ClustAssess/issues",
  "Config/testthat/edition": "3",
  "Config/roxygen2/version": "8.1.0",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make\nlibharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev libssl-dev python3\nzlib1g-dev",
  "Repository": "https://core-bioinformatics.r-universe.dev",
  "Date/Publication": "2026-08-29 19:56:24 UTC",
  "RemoteUrl": "https://github.com/core-bioinformatics/clustassess",
  "RemoteRef": "HEAD",
  "RemoteSha": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-09-28 12:55:24 UTC",
    "User": "root"
  },
  "Author": "Andi Munteanu [aut, cre],\nArash Shahsavari [aut],\nRafael Kollyfas [ctb],\nMiguel Larraz Lopez de Novales [aut],\nLiviu Ciortuz [ctb],\nIrina Mohorianu [aut]",
  "Maintainer": "Andi Munteanu <am3019@cam.ac.uk>",
  "_user": "core-bioinformatics",
  "_type": "src",
  "_file": "ClustAssess_1.2.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d9604f8dd8df740e3327f86613e56b7a464563a66736e3d421a8369a9d13eaf0",
  "_filesize": 455965,
  "_sha256": "d9604f8dd8df740e3327f86613e56b7a464563a66736e3d421a8369a9d13eaf0",
  "_expires": "2027-01-06T13:06:22.000Z",
  "_created": "2026-09-28T12:55:24.000Z",
  "_published": "2026-09-28T13:06:24.299Z",
  "_jobs": [
    {
      "job": 108936852011,
      "time": 299,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10971527407"
    },
    {
      "job": 108936852010,
      "time": 374,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10970958894"
    },
    {
      "job": 108936852099,
      "time": 311,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10970833205"
    },
    {
      "job": 108936852007,
      "time": 365,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10971323356"
    },
    {
      "job": 108936851865,
      "time": 289,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10971282761"
    },
    {
      "job": 108936852017,
      "time": 585,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10971523234"
    },
    {
      "job": 108936852036,
      "time": 335,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10971337785"
    },
    {
      "job": 108936851912,
      "time": 587,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10971458429"
    },
    {
      "job": 108934859019,
      "time": 322,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10971401781"
    },
    {
      "job": 108936851819,
      "time": 197,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10971208063"
    },
    {
      "job": 108936851995,
      "time": 521,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10971523061"
    },
    {
      "job": 108936851894,
      "time": 329,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10971666829"
    },
    {
      "job": 108936851852,
      "time": 282,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10971088399"
    },
    {
      "job": 108936852137,
      "time": 532,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10971423528"
    },
    {
      "job": 108936851880,
      "time": 311,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10971323210"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855",
  "_status": "success",
  "_upstream": "https://github.com/core-bioinformatics/clustassess",
  "_commit": {
    "id": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
    "author": "AndiMunteanu <munteanu_andi98@yahoo.com>",
    "committer": "AndiMunteanu <munteanu_andi98@yahoo.com>",
    "message": "Merge branch 'main' of https://github.com/Core-Bioinformatics/ClustAssess\n",
    "time": 1788033384
  },
  "_maintainer": {
    "name": "Andi Munteanu",
    "email": "am3019@cam.ac.uk"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "fastcluster",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "Gmedian",
      "role": "Imports"
    },
    {
      "package": "ggnewscale",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrastr",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "gprofiler2",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "leiden",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "version": ">= 1.5.0",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "progress",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "paletteer",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "qualpalr",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "RANN",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "Seurat",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "shinyjs",
      "role": "Imports"
    },
    {
      "package": "shinyLP",
      "role": "Imports"
    },
    {
      "package": "shinyWidgets",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "uwot",
      "role": "Imports"
    },
    {
      "package": "vioplot",
      "role": "Imports"
    },
    {
      "package": "zip",
      "role": "Imports"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "colourpicker",
      "role": "Suggests"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Suggests"
    },
    {
      "package": "data.table",
      "role": "Suggests"
    },
    {
      "package": "DelayedMatrixStats",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "doParallel",
      "role": "Suggests"
    },
    {
      "package": "leidenbase",
      "role": "Suggests"
    },
    {
      "package": "monocle3",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "ragg",
      "role": "Suggests"
    },
    {
      "package": "reticulate",
      "role": "Suggests"
    },
    {
      "package": "rhdf5",
      "role": "Suggests"
    },
    {
      "package": "RhpcBLASctl",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "scales",
      "role": "Suggests"
    },
    {
      "package": "SeuratObject",
      "role": "Suggests"
    },
    {
      "package": "SharedObject",
      "role": "Suggests"
    },
    {
      "package": "styler",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "core-bioinformatics",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-35",
      "n": 15
    }
  ],
  "_tags": [
    {
      "name": "v1.2.0",
      "date": "2026-08-29"
    }
  ],
  "_topics": [
    "software",
    "singlecell",
    "rnaseq",
    "atacseq",
    "normalization",
    "preprocessing",
    "dimensionreduction",
    "visualization",
    "qualitycontrol",
    "clustering",
    "classification",
    "annotation",
    "geneexpression",
    "differentialexpression",
    "bioinformatics",
    "genomics",
    "machine-learning",
    "parameter-optimization",
    "robustness",
    "single-cell",
    "unsupervised-learning",
    "cpp"
  ],
  "_stars": 34,
  "_contributors": [
    {
      "user": "andimunteanu",
      "count": 482,
      "uuid": 33558614
    },
    {
      "user": "sharash",
      "count": 112,
      "uuid": 26744758
    },
    {
      "user": "miguellarraz",
      "count": 36,
      "uuid": 67822283
    }
  ],
  "_userbio": {
    "uuid": 71281163,
    "type": "organization",
    "name": "Core Bioinformatics group",
    "followers": 28
  },
  "_downloads": {
    "count": 608,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ClustAssess"
  },
  "_devurl": "https://github.com/core-bioinformatics/clustassess",
  "_pkgdown": "https://core-bioinformatics.github.io/ClustAssess/",
  "_searchresults": 14,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/ClustAssess.html",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/core-bioinformatics/clustassess",
  "_realowner": "core-bioinformatics",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2021-03-31"
    },
    {
      "version": "0.1.1",
      "date": "2021-03-31"
    },
    {
      "version": "0.3.0",
      "date": "2022-01-26"
    },
    {
      "version": "1.0.0",
      "date": "2025-01-31"
    },
    {
      "version": "1.1.0",
      "date": "2025-05-27"
    },
    {
      "version": "1.2.0",
      "date": "2026-09-08"
    }
  ],
  "_exports": [
    "add_metadata",
    "assess_clustering_stability",
    "assess_feature_stability",
    "assess_nn_stability",
    "automatic_stability_assessment",
    "calculate_markers",
    "calculate_markers_shiny",
    "choose_stable_clusters",
    "consensus_cluster",
    "create_monocle_default",
    "create_monocle_from_clustassess",
    "create_monocle_from_clustassess_app",
    "create_seurat_object_default",
    "create_seurat_object_from_clustassess_app",
    "element_agreement",
    "element_consistency",
    "element_sim",
    "element_sim_elscore",
    "element_sim_matrix",
    "get_clusters_from_clustassess_object",
    "get_highest_prune_param",
    "get_highest_prune_param_embedding",
    "get_nn_conn_comps",
    "getNNmatrix",
    "marker_overlap",
    "merge_partitions",
    "pac_convergence",
    "pac_landscape",
    "plot_clust_hierarchical",
    "plot_clustering_overall_stability",
    "plot_clustering_per_value_stability",
    "plot_connected_comps_evolution",
    "plot_feature_overall_stability_boxplot",
    "plot_feature_overall_stability_incremental",
    "plot_feature_per_resolution_stability_boxplot",
    "plot_feature_per_resolution_stability_incremental",
    "plot_feature_stability_ecs_facet",
    "plot_feature_stability_mb_facet",
    "plot_k_n_partitions",
    "plot_k_resolution_corresp",
    "plot_n_neigh_ecs",
    "plot_n_neigh_k_correspondence",
    "server_comparisons",
    "server_dimensionality_reduction",
    "server_graph_clustering",
    "server_graph_construction",
    "server_landing_page",
    "server_sandbox",
    "ui_comparisons",
    "ui_dimensionality_reduction",
    "ui_graph_clustering",
    "ui_graph_construction",
    "ui_landing_page",
    "ui_sandbox",
    "weighted_element_consistency",
    "write_objects",
    "write_shiny_app"
  ],
  "_help": [
    {
      "page": "add_metadata",
      "title": "Add metadata to ClustAssess ShinyApp",
      "topics": [
        "add_metadata"
      ]
    },
    {
      "page": "assess_clustering_stability",
      "title": "Assessment of Stability for Graph Clustering",
      "topics": [
        "assess_clustering_stability"
      ]
    },
    {
      "page": "assess_feature_stability",
      "title": "Assess the stability for configurations of feature types and sizes",
      "topics": [
        "assess_feature_stability"
      ]
    },
    {
      "page": "assess_nn_stability",
      "title": "Assess the stability for Graph Building Parameters",
      "topics": [
        "assess_nn_stability"
      ]
    },
    {
      "page": "automatic_stability_assessment",
      "title": "Assessment of Stability for Graph Clustering",
      "topics": [
        "automatic_stability_assessment"
      ]
    },
    {
      "page": "calculate_markers",
      "title": "Calculate markers",
      "topics": [
        "calculate_markers"
      ]
    },
    {
      "page": "calculate_markers_shiny",
      "title": "Calculate markers - Shiny",
      "topics": [
        "calculate_markers_shiny"
      ]
    },
    {
      "page": "choose_stable_clusters",
      "title": "Choose stable clusters based on ECC and frequency",
      "topics": [
        "choose_stable_clusters"
      ]
    },
    {
      "page": "consensus_cluster",
      "title": "Consensus Clustering and Proportion of Ambiguously Clustered Pairs",
      "topics": [
        "consensus_cluster"
      ]
    },
    {
      "page": "create_monocle_default",
      "title": "Create monocle object",
      "topics": [
        "create_monocle_default"
      ]
    },
    {
      "page": "create_monocle_from_clustassess",
      "title": "Create monocle object from a ClustAssess object",
      "topics": [
        "create_monocle_from_clustassess"
      ]
    },
    {
      "page": "create_monocle_from_clustassess_app",
      "title": "Create monocle object from a ClustAssess shiny app",
      "topics": [
        "create_monocle_from_clustassess_app"
      ]
    },
    {
      "page": "create_seurat_object_default",
      "title": "Create Seurat object",
      "topics": [
        "create_seurat_object_default"
      ]
    },
    {
      "page": "create_seurat_object_from_clustassess_app",
      "title": "Create Seurat object from a ClustAssess shiny app",
      "topics": [
        "create_seurat_object_from_clustassess_app"
      ]
    },
    {
      "page": "element_agreement",
      "title": "Element-Wise Average Agreement Between a Set of Clusterings",
      "topics": [
        "element_agreement"
      ]
    },
    {
      "page": "element_consistency",
      "title": "Element-Wise Consistency Between a Set of Clusterings",
      "topics": [
        "element_consistency"
      ]
    },
    {
      "page": "element_sim",
      "title": "The Element-Centric Clustering Similarity",
      "topics": [
        "element_sim"
      ]
    },
    {
      "page": "element_sim_elscore",
      "title": "The Element-Centric Clustering Similarity for each Element",
      "topics": [
        "element_sim_elscore"
      ]
    },
    {
      "page": "element_sim_matrix",
      "title": "Pairwise Comparison of Clusterings",
      "topics": [
        "element_sim_matrix"
      ]
    },
    {
      "page": "get_clusters_from_clustassess_object",
      "title": "Extract config-specific clusters from a ClustAssess object",
      "topics": [
        "get_clusters_from_clustassess_object"
      ]
    },
    {
      "page": "get_colour_vector_from_palette",
      "title": "Get the vector of colours from a palette",
      "topics": [
        "get_colour_vector_from_palette"
      ]
    },
    {
      "page": "get_highest_prune_param",
      "title": "Calculate the highest pruning parameter for the SNN graph given NN matrix",
      "topics": [
        "get_highest_prune_param"
      ]
    },
    {
      "page": "get_highest_prune_param_embedding",
      "title": "Calculate the highest pruning parameter for the SNN graph given Embedding",
      "topics": [
        "get_highest_prune_param_embedding"
      ]
    },
    {
      "page": "get_nn_conn_comps",
      "title": "Relationship Between Nearest Neighbours and Connected Components",
      "topics": [
        "get_nn_conn_comps"
      ]
    },
    {
      "page": "getNNmatrix",
      "title": "Computes the NN adjacency matrix given the neighbours",
      "topics": [
        "getNNmatrix"
      ]
    },
    {
      "page": "marker_overlap",
      "title": "Cell-Wise Marker Gene Overlap",
      "topics": [
        "marker_overlap"
      ]
    },
    {
      "page": "merge_partitions",
      "title": "Merge Partitions",
      "topics": [
        "merge_partitions"
      ]
    },
    {
      "page": "merge_resolutions",
      "title": "Merge Partitions from different Resolutions",
      "topics": [
        "merge_resolutions"
      ]
    },
    {
      "page": "pac_convergence",
      "title": "PAC Convergence Plot",
      "topics": [
        "pac_convergence"
      ]
    },
    {
      "page": "pac_landscape",
      "title": "PAC Landscape Plot",
      "topics": [
        "pac_landscape"
      ]
    },
    {
      "page": "plot_clust_hierarchical",
      "title": "Hierarchical relationship between partitions with different number of clusters",
      "topics": [
        "plot_clust_hierarchical"
      ]
    },
    {
      "page": "plot_clustering_difference_facet",
      "title": "Clustering Method Stability Facet Plot",
      "topics": [
        "plot_clustering_difference_facet"
      ]
    },
    {
      "page": "plot_clustering_overall_stability",
      "title": "Clustering Method Overall Stability Boxplot",
      "topics": [
        "plot_clustering_overall_stability"
      ]
    },
    {
      "page": "plot_clustering_per_value_stability",
      "title": "Clustering Method per value Stability Boxplot",
      "topics": [
        "plot_clustering_per_value_stability"
      ]
    },
    {
      "page": "plot_connected_comps_evolution",
      "title": "Relationship Between Number of Nearest Neighbours and Graph Connectivity",
      "topics": [
        "plot_connected_comps_evolution"
      ]
    },
    {
      "page": "plot_feature_overall_stability_boxplot",
      "title": "Overall Feature Stability Boxplot",
      "topics": [
        "plot_feature_overall_stability_boxplot"
      ]
    },
    {
      "page": "plot_feature_overall_stability_incremental",
      "title": "Overall Feature Stability Incremental Boxplot",
      "topics": [
        "plot_feature_overall_stability_incremental"
      ]
    },
    {
      "page": "plot_feature_per_resolution_stability_boxplot",
      "title": "Per resolution Feature Stability Boxplot",
      "topics": [
        "plot_feature_per_resolution_stability_boxplot"
      ]
    },
    {
      "page": "plot_feature_per_resolution_stability_incremental",
      "title": "Per resolution - Feature Stability Incremental Boxplot",
      "topics": [
        "plot_feature_per_resolution_stability_incremental"
      ]
    },
    {
      "page": "plot_feature_stability_ecs_facet",
      "title": "Feature Stability - EC Consistency Facet Plot",
      "topics": [
        "plot_feature_stability_ecs_facet"
      ]
    },
    {
      "page": "plot_feature_stability_mb_facet",
      "title": "Feature Stability - Cluster Membership Facet Plot",
      "topics": [
        "plot_feature_stability_mb_facet"
      ]
    },
    {
      "page": "plot_k_n_partitions",
      "title": "Relationship Between the Number of Clusters and the Number of Unique Partitions",
      "topics": [
        "plot_k_n_partitions"
      ]
    },
    {
      "page": "plot_k_resolution_corresp",
      "title": "Correspondence Between Resolution and the Number of Clusters",
      "topics": [
        "plot_k_resolution_corresp"
      ]
    },
    {
      "page": "plot_n_neigh_ecs",
      "title": "Graph construction parameters - ECC facet",
      "topics": [
        "plot_n_neigh_ecs"
      ]
    },
    {
      "page": "plot_n_neigh_k_correspondence",
      "title": "Relationship Between Number of Nearest Neighbours and Number of Clusters",
      "topics": [
        "plot_n_neigh_k_correspondence"
      ]
    },
    {
      "page": "server_comparisons",
      "title": "Server - Comparison module",
      "topics": [
        "server_comparisons"
      ]
    },
    {
      "page": "server_dimensionality_reduction",
      "title": "Server - Dimensionality reduction module",
      "topics": [
        "server_dimensionality_reduction"
      ]
    },
    {
      "page": "server_graph_clustering",
      "title": "Server - Graph clustering module",
      "topics": [
        "server_graph_clustering"
      ]
    },
    {
      "page": "server_graph_construction",
      "title": "Server - Graph construction module",
      "topics": [
        "server_graph_construction"
      ]
    },
    {
      "page": "server_landing_page",
      "title": "Server - Landing page module",
      "topics": [
        "server_landing_page"
      ]
    },
    {
      "page": "server_sandbox",
      "title": "Server - Sandbox module",
      "topics": [
        "server_sandbox"
      ]
    },
    {
      "page": "ui_comparisons",
      "title": "UI - Comparison module",
      "topics": [
        "ui_comparisons"
      ]
    },
    {
      "page": "ui_dimensionality_reduction",
      "title": "UI - Dimensionality reduction module",
      "topics": [
        "ui_dimensionality_reduction"
      ]
    },
    {
      "page": "ui_graph_clustering",
      "title": "UI - Graph clustering module",
      "topics": [
        "ui_graph_clustering"
      ]
    },
    {
      "page": "ui_graph_construction",
      "title": "UI - Graph construction module",
      "topics": [
        "ui_graph_construction"
      ]
    },
    {
      "page": "ui_landing_page",
      "title": "UI - Landing page module",
      "topics": [
        "ui_landing_page"
      ]
    },
    {
      "page": "ui_sandbox",
      "title": "UI - Sandbox module",
      "topics": [
        "ui_sandbox"
      ]
    },
    {
      "page": "weighted_element_consistency",
      "title": "Weighted Element-Centric Consistency",
      "topics": [
        "weighted_element_consistency"
      ]
    },
    {
      "page": "write_objects",
      "title": "Write the objects for the ClustAssess ShinyApp",
      "topics": [
        "write_objects"
      ]
    },
    {
      "page": "write_shiny_app",
      "title": "Create the ClustAssess ShinyApp",
      "topics": [
        "write_shiny_app",
        "write_shiny_app.default",
        "write_shiny_app.Seurat"
      ]
    }
  ],
  "_readme": "https://github.com/core-bioinformatics/clustassess/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "base64enc",
    "beeswarm",
    "BH",
    "bitops",
    "bslib",
    "cachem",
    "Cairo",
    "caTools",
    "cli",
    "cluster",
    "codetools",
    "commonmark",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "deldir",
    "DEoptimR",
    "digest",
    "dotCall64",
    "dplyr",
    "dqrng",
    "DT",
    "evaluate",
    "farver",
    "fastcluster",
    "fastDummies",
    "fastmap",
    "fitdistrplus",
    "FNN",
    "fontawesome",
    "foreach",
    "fs",
    "future",
    "future.apply",
    "generics",
    "ggbeeswarm",
    "ggnewscale",
    "ggplot2",
    "ggrastr",
    "ggrepel",
    "ggridges",
    "globals",
    "glue",
    "Gmedian",
    "goftest",
    "gplots",
    "gprofiler2",
    "gridExtra",
    "gtable",
    "gtools",
    "here",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "ica",
    "igraph",
    "irlba",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "leiden",
    "lifecycle",
    "listenv",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixStats",
    "memoise",
    "mime",
    "miniUI",
    "nlme",
    "openssl",
    "otel",
    "paletteer",
    "parallelly",
    "patchwork",
    "pbapply",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polyclip",
    "prettyunits",
    "prismatic",
    "progress",
    "progressr",
    "promises",
    "purrr",
    "qualpalr",
    "R6",
    "ragg",
    "RANN",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppHNSW",
    "RcppProgress",
    "RcppTOML",
    "RCurl",
    "rematch2",
    "reshape2",
    "reticulate",
    "rlang",
    "rmarkdown",
    "robustbase",
    "ROCR",
    "rprojroot",
    "RSpectra",
    "rstudioapi",
    "Rtsne",
    "S7",
    "sass",
    "scales",
    "scattermore",
    "sctransform",
    "Seurat",
    "SeuratObject",
    "shiny",
    "shinyjs",
    "shinyLP",
    "shinyWidgets",
    "sitmo",
    "sm",
    "sourcetools",
    "sp",
    "spam",
    "spatstat.data",
    "spatstat.explore",
    "spatstat.geom",
    "spatstat.random",
    "spatstat.sparse",
    "spatstat.univar",
    "spatstat.utils",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "systemfonts",
    "tensor",
    "textshaping",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "uwot",
    "vctrs",
    "vioplot",
    "vipor",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "yaml",
    "zip",
    "zoo"
  ],
  "_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": 4.6776069527204935,
  "_indexed": true,
  "_nocasepkg": "clustassess",
  "_universes": [
    "core-bioinformatics"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.0",
      "date": "2026-09-28T12:59:12.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/621145a3352c9ad4bc9f3ca3cd698b93d28664737383f019f0a546193cf671a8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.0",
      "date": "2026-09-28T12:59:43.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/cf50ab9bca928b2dd5b39251905d844df77ac0bac48e94b52920ceba694f5227",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.2.0",
      "date": "2026-09-28T12:59:32.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/a97e69e8fb2b35834c5ceaf0f9c7fa1ab93ef075e477d0f16f602ad7e82df307",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.2.0",
      "date": "2026-09-28T12:59:33.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/3e935a64f605b4b44e1a96863c548bb3c1f8f510f911e39268e9175c75c61243",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.0",
      "date": "2026-09-28T12:58:27.000Z",
      "arch": "aarch64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/45c164a6b2980d93bc47efe559e7e405eff8d95862cb3b9e18532a4e837f2625",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.0",
      "date": "2026-09-28T13:01:25.000Z",
      "arch": "x86_64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/1263851d42da48aa48297d3fae5c76264ab100db702060bd6f4bee182bbe0240",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.2.0",
      "date": "2026-09-28T12:58:36.000Z",
      "arch": "aarch64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/a09290fb904f46f341c7eeed88d6d00986c1b61fcdf545febd799fe7925c56cb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.2.0",
      "date": "2026-09-28T13:00:40.000Z",
      "arch": "x86_64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/4f986e4085e9db9229c67229689e4c84fbe26788e702d2d9d3241be3f3b16045",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.0",
      "date": "2026-09-28T12:59:11.000Z",
      "arch": "emscripten",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/c3a2e8514880c4018728d967cf8122b1e93c0aa77020443cf3bafe15b1c8791d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-09-28T13:01:22.000Z",
      "arch": "aarch64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/9101d8e257a8dc520b56e538d7cd295c10d4bdcacbd172b9b0f42d9b40af42cf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-09-28T12:57:39.000Z",
      "arch": "x86_64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/bdf333a2e72c37e594e6b1b46ec898b5d55b8cbb2ad6e947301e65278067e543",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-09-28T12:57:32.000Z",
      "arch": "x86_64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/ff3dc813ff15454614dc826f5dd7974b180360511a033b692c3626b8759ff7df",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-09-28T13:01:42.000Z",
      "arch": "aarch64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/a3502b1d4c49c31b8ec96efe4473c85fb7bf86580349778c9fe6016316c061bb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-09-28T12:58:44.000Z",
      "arch": "x86_64",
      "commit": "142d534c129ad68644593b0a0f67d4cb70d12f2f",
      "fileid": "https://r2.ropensci.org/d5177fc78b81389c7c1594f893717afd81b7a44aa6f5b8153476fe534b112e2d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/core-bioinformatics/actions/runs/36424399855"
    }
  ]
}