{
  "_id": "6a47aecee06c18f0a651ad05",
  "Package": "destiny",
  "Type": "Package",
  "Title": "Creates diffusion maps",
  "Version": "3.27.0",
  "Date": "2014-12-19",
  "Authors@R": "c(\nperson('Philipp', 'Angerer', NULL, 'phil.angerer@gmail.com', c('cre', 'aut'), comment = c(ORCID = '0000-0002-0369-2888')),\nperson('Laleh', 'Haghverdi', NULL, 'laleh.haghverdi@helmholtz-muenchen.de', 'ctb'),\nperson('Maren', 'Büttner', NULL, 'maren.buettner@helmholtz-muenchen.de', 'ctb', comment = c(ORCID = '0000-0002-6189-3792')),\nperson('Fabian', 'Theis', NULL, 'fabian.theis@helmholtz-muenchen.de', 'ctb', comment = c(ORCID = '0000-0002-2419-1943')),\nperson('Carsten', 'Marr', NULL, 'carsten.marr@helmholtz-muenchen.de', 'ctb', comment = c(ORCID = '0000-0003-2154-4552')),\nperson('Florian', 'Büttner', NULL, 'f.buettner@helmholtz-muenchen.de', 'ctb', comment = c(ORCID = '0000-0001-5587-6761')))",
  "Description": "Create and plot diffusion maps.",
  "License": "GPL-3",
  "URL": "https://github.com/theislab/destiny/,\nhttps://bioconductor.org/packages/destiny,\nhttps://doi.org/10.1093/bioinformatics/btv715",
  "BugReports": "https://github.com/theislab/destiny/issues",
  "Encoding": "UTF-8",
  "SystemRequirements": "C++11",
  "NeedsCompilation": "yes",
  "VignetteBuilder": "knitr",
  "biocViews": "CellBiology, CellBasedAssays, Clustering, Software,\nVisualization",
  "Collate": "'RcppExports.R' 'aaa.r' 'accessor-generics.r' 'censoring.r'\n'colorlegend.r' 'cube_helix.r' 'dataset-helpers.r'\n'destiny-package.r' 's4-unions.r' 'dist-matrix-coerce.r'\n'sigmas.r' 'diffusionmap.r' 'diffusionmap-methods-accession.r'\n'diffusionmap-methods.r' 'plothelpers.r'\n'diffusionmap-plotting.r' 'dpt-branching.r' 'dpt-helpers.r'\n'dpt.r' 'dpt-methods-matrix.r' 'dpt-methods.r' 'utils.r'\n'dpt-plotting.r' 'eig_decomp.r' 'expressionset-helpers.r'\n'find_dm_k.r' 'gene-relevance.r' 'gene-relevance-methods.r'\n'gene-relevance-plotting-differential-map.r'\n'gene-relevance-plotting-gr-map.r'\n'gene-relevance-plotting-rank.r' 'gene-relevance-plotting.r'\n'guo-data.r' 'knn.r' 'l_which.r' 'methods-coercion.r'\n'methods-extraction.r' 'methods-update.r' 'predict.r'\n'projection-dist.r' 'rankcor.r' 'sigmas-plotting.r'\n'smth-gaussian.r'",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "cmake make libicu-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-07-03 08:21:54 UTC",
  "RemoteUrl": "https://github.com/bioc/destiny",
  "RemoteRef": "HEAD",
  "RemoteSha": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
  "Packaged": {
    "Date": "2026-07-03 12:15:44 UTC",
    "User": "root"
  },
  "Author": "Philipp Angerer [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-0369-2888>),\nLaleh Haghverdi [ctb],\nMaren Büttner [ctb] (ORCID: <https://orcid.org/0000-0002-6189-3792>),\nFabian Theis [ctb] (ORCID: <https://orcid.org/0000-0002-2419-1943>),\nCarsten Marr [ctb] (ORCID: <https://orcid.org/0000-0003-2154-4552>),\nFlorian Büttner [ctb] (ORCID: <https://orcid.org/0000-0001-5587-6761>)",
  "Maintainer": "Philipp Angerer <phil.angerer@gmail.com>",
  "MD5sum": "7b3ee18f7929da962a4a212193ce5798",
  "_user": "bioc",
  "_type": "src",
  "_file": "destiny_3.27.0.tar.gz",
  "_fileid": "20fbd05700454a79a69961111baad42c4db847c9cd6d8c8540a04de4509c6da9",
  "_filesize": 528173,
  "_sha256": "20fbd05700454a79a69961111baad42c4db847c9cd6d8c8540a04de4509c6da9",
  "_created": "2026-07-03T12:15:44.000Z",
  "_published": "2026-07-03T12:45:01.990Z",
  "_jobs": [
    {
      "job": 84998031122,
      "time": 339,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8066354425"
    },
    {
      "job": 84998031422,
      "time": 428,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8066385073"
    },
    {
      "job": 84998031238,
      "time": 526,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8066414440"
    },
    {
      "job": 84998031254,
      "time": 430,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8066384756"
    },
    {
      "job": 84998031392,
      "time": 518,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8066411638"
    },
    {
      "job": 84998031172,
      "time": 232,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8066386088"
    },
    {
      "job": 84998031168,
      "time": 590,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8066475986"
    },
    {
      "job": 84998031178,
      "time": 319,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8066385430"
    },
    {
      "job": 84998031219,
      "time": 494,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8066455529"
    },
    {
      "job": 84996824450,
      "time": 450,
      "config": "source",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8066244159"
    },
    {
      "job": 84998031093,
      "time": 302,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8066343404"
    },
    {
      "job": 84998031176,
      "time": 1668,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8066804916"
    },
    {
      "job": 84998031157,
      "time": 1630,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8066791682"
    },
    {
      "job": 84998031159,
      "time": 1616,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8066787349"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/destiny",
  "_commit": {
    "id": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
    "author": "Philipp A <flying-sheep@web.de>",
    "committer": "Philipp A <flying-sheep@web.de>",
    "message": "style and conflicts\n",
    "time": 1783066914
  },
  "_maintainer": {
    "name": "Philipp Angerer",
    "email": "phil.angerer@gmail.com",
    "login": "flying-sheep",
    "orcid": "0000-0002-0369-2888",
    "description": "",
    "uuid": 291575
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "grDevices",
      "role": "LinkingTo"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.10.3",
      "role": "Imports"
    },
    {
      "package": "RcppEigen",
      "role": "Imports"
    },
    {
      "package": "RSpectra",
      "version": ">= 0.14-0",
      "role": "Imports"
    },
    {
      "package": "irlba",
      "role": "Imports"
    },
    {
      "package": "pcaMethods",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggplot.multistats",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "role": "Imports"
    },
    {
      "package": "ggthemes",
      "role": "Imports"
    },
    {
      "package": "VIM",
      "role": "Imports"
    },
    {
      "package": "knn.covertree",
      "role": "Imports"
    },
    {
      "package": "proxy",
      "role": "Imports"
    },
    {
      "package": "RcppHNSW",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "scatterplot3d",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "igraph",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "FNN",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "gridExtra",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    },
    {
      "package": "conflicted",
      "role": "Suggests"
    },
    {
      "package": "viridis",
      "role": "Suggests"
    },
    {
      "package": "rgl",
      "role": "Suggests"
    },
    {
      "package": "scRNAseq",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "scran",
      "role": "Suggests"
    },
    {
      "package": "repr",
      "role": "Suggests"
    },
    {
      "package": "rgl",
      "role": "Enhances"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Enhances"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-45",
      "n": 1
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-27",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "3.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "3.26.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "cellbiology",
    "cellbasedassays",
    "clustering",
    "software",
    "visualization",
    "diffusion-maps",
    "dimensionality-reduction",
    "cpp"
  ],
  "_stars": 107,
  "_contributors": [
    {
      "user": "flying-sheep",
      "count": 226,
      "uuid": 291575
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "dtenenba",
      "count": 4,
      "uuid": 2286826
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "lshep",
      "count": 1,
      "uuid": 18724380
    },
    {
      "user": "loyale",
      "count": 1,
      "uuid": 1261153
    },
    {
      "user": "sonali-bioc",
      "count": 1,
      "uuid": 6373953
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 18,
  "_devurl": "https://github.com/theislab/destiny",
  "_searchresults": 1046,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/destiny.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/theislab/destiny",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "as.data.frame",
    "as.ExpressionSet",
    "as.matrix",
    "branch_divide",
    "colorlegend",
    "cube_helix",
    "dataset",
    "dataset<-",
    "DiffusionMap",
    "distance",
    "distance<-",
    "dm_predict",
    "DPT",
    "eig_decomp",
    "eigenvalues",
    "eigenvalues<-",
    "eigenvectors",
    "eigenvectors<-",
    "featureNames",
    "featureNames<-",
    "find_dm_k",
    "find_knn",
    "find_sigmas",
    "find_tips",
    "fortify.DiffusionMap",
    "fortify.DPT",
    "gene_relevance",
    "l_which",
    "ncol",
    "nrow",
    "optimal_sigma",
    "plot",
    "plot_differential_map",
    "plot_gene_relevance",
    "plot_gene_relevance_rank",
    "plot.DiffusionMap",
    "plot.DPT",
    "print",
    "projection_dist",
    "random_root",
    "read.ExpressionSet",
    "scale_color_cube_helix",
    "scale_colour_cube_helix",
    "scale_fill_cube_helix",
    "show",
    "sigmas",
    "Sigmas",
    "sigmas<-",
    "tips",
    "updateObject"
  ],
  "_datasets": [
    {
      "name": "guo",
      "title": "Guo at al. mouse embryonic stem cell qPCR data",
      "object": "guo",
      "file": "guo.rda",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "guo_norm",
      "title": "Guo at al. mouse embryonic stem cell qPCR data",
      "object": "guo_norm",
      "file": "guo_norm.rda",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "coercions",
      "title": "Coercion methods",
      "topics": [
        "as.data.frame,DiffusionMap-method",
        "as.data.frame,DPT-method",
        "as.data.frame.DiffusionMap",
        "as.data.frame.DPT",
        "as.matrix,DPT-method",
        "as.matrix.DPT",
        "Coercion methods",
        "fortify.DiffusionMap",
        "fortify.DPT"
      ]
    },
    {
      "page": "colorlegend",
      "title": "Color legend",
      "topics": [
        "colorlegend"
      ]
    },
    {
      "page": "cube_helix",
      "title": "Sequential color palette using the cube helix system",
      "topics": [
        "cube_helix",
        "scale_color_cube_helix",
        "scale_colour_cube_helix",
        "scale_fill_cube_helix"
      ]
    },
    {
      "page": "destiny",
      "title": "Create and plot diffusion maps",
      "topics": [
        "destiny-package",
        "destiny"
      ]
    },
    {
      "page": "destiny-generics",
      "title": "destiny generics",
      "topics": [
        "dataset",
        "dataset<-",
        "destiny generics",
        "distance",
        "distance<-",
        "eigenvalues",
        "eigenvalues<-",
        "eigenvectors",
        "eigenvectors<-",
        "optimal_sigma",
        "sigmas",
        "sigmas<-"
      ]
    },
    {
      "page": "DiffusionMap-accessors",
      "title": "DiffusionMap accession methods",
      "topics": [
        "dataset,DiffusionMap-method",
        "dataset<-,DiffusionMap-method",
        "DiffusionMap accession methods",
        "distance,DiffusionMap-method",
        "distance<-,DiffusionMap-method",
        "eigenvalues,DiffusionMap-method",
        "eigenvalues<-,DiffusionMap-method",
        "eigenvectors,DiffusionMap-method",
        "eigenvectors<-,DiffusionMap-method",
        "optimal_sigma,DiffusionMap-method",
        "sigmas,DiffusionMap-method",
        "sigmas<-,DiffusionMap-method"
      ]
    },
    {
      "page": "DiffusionMap-methods",
      "title": "DiffusionMap methods",
      "topics": [
        "DiffusionMap methods",
        "print,DiffusionMap-method",
        "print.DiffusionMap",
        "show,DiffusionMap-method",
        "show.DiffusionMap"
      ]
    },
    {
      "page": "DiffusionMap-class",
      "title": "Create a diffusion map of cells",
      "topics": [
        "DiffusionMap",
        "DiffusionMap-class"
      ]
    },
    {
      "page": "dm_predict",
      "title": "Predict new data points using an existing DiffusionMap. The resulting matrix can be used in the plot method for the DiffusionMap",
      "topics": [
        "dm_predict"
      ]
    },
    {
      "page": "DPT-matrix-methods",
      "title": "DPT Matrix methods",
      "topics": [
        "dim,DPT-method",
        "dim.DPT",
        "DPT matrix methods",
        "ncol,DPT-method",
        "ncol.DPT",
        "nrow,DPT-method",
        "nrow.DPT",
        "[,DPT,index,index,logicalOrMissing-method",
        "[,DPT,index,missing,logicalOrMissing-method",
        "[,DPT,missing,index,logicalOrMissing-method",
        "[,DPT,missing,missing,logicalOrMissing-method",
        "[.DPT",
        "[[,DPT,index,index-method"
      ]
    },
    {
      "page": "DPT-methods",
      "title": "DPT methods",
      "topics": [
        "branch_divide",
        "dataset,DPT-method",
        "dataset.DPT",
        "dataset<-,DPT-method",
        "DPT methods",
        "tips"
      ]
    },
    {
      "page": "DPT",
      "title": "Diffusion Pseudo Time",
      "topics": [
        "DPT",
        "DPT-class"
      ]
    },
    {
      "page": "eig_decomp",
      "title": "Fast eigen decomposition using 'eigs'",
      "topics": [
        "eig_decomp"
      ]
    },
    {
      "page": "ExpressionSet-helpers",
      "title": "Convert object to ExpressionSet or read it from a file",
      "topics": [
        "as.ExpressionSet",
        "as.ExpressionSet,data.frame-method",
        "ExpressionSet helper methods",
        "read.ExpressionSet"
      ]
    },
    {
      "page": "extractions",
      "title": "Extraction methods",
      "topics": [
        "$,DiffusionMap-method",
        "$,DPT-method",
        "$.DiffusionMap",
        "$.DPT",
        "Extraction methods",
        "names,DiffusionMap-method",
        "names,DPT-method",
        "names.DiffusionMap",
        "names.DPT",
        "[[,DiffusionMap,character,missing-method",
        "[[,DPT,character,missing-method",
        "[[.DiffusionMap",
        "[[.DPT"
      ]
    },
    {
      "page": "find_dm_k",
      "title": "Find a suitable k",
      "topics": [
        "find_dm_k"
      ]
    },
    {
      "page": "knn",
      "title": "kNN search",
      "topics": [
        "find_knn"
      ]
    },
    {
      "page": "find_sigmas",
      "title": "Calculate the average dimensionality for m different gaussian kernel widths (sigma).",
      "topics": [
        "find_sigmas"
      ]
    },
    {
      "page": "find_tips",
      "title": "Find tips in a DiffusionMap object",
      "topics": [
        "find_tips"
      ]
    },
    {
      "page": "Gene-Relevance-methods",
      "title": "Gene Relevance methods",
      "topics": [
        "dataset,GeneRelevance-method",
        "dataset.GeneRelevance",
        "dataset<-,GeneRelevance-method",
        "distance,GeneRelevance-method",
        "distance<-,GeneRelevance-method",
        "featureNames,GeneRelevance-method",
        "featureNames.GeneRelevance",
        "featureNames<-,GeneRelevance,characterOrFactor-method",
        "Gene Relevance methods",
        "print,GeneRelevance-method",
        "show,GeneRelevance-method"
      ]
    },
    {
      "page": "Gene-Relevance",
      "title": "Gene relevances for entire data set",
      "topics": [
        "GeneRelevance-class",
        "gene_relevance",
        "gene_relevance,DiffusionMap,missing-method",
        "gene_relevance,matrix,dMatrixOrMatrix-method"
      ]
    },
    {
      "page": "guo",
      "title": "Guo at al. mouse embryonic stem cell qPCR data",
      "topics": [
        "data:guo",
        "data:guo_norm",
        "guo",
        "guo_norm"
      ]
    },
    {
      "page": "l_which",
      "title": "Logical which",
      "topics": [
        "l_which"
      ]
    },
    {
      "page": "Gene-Relevance-plotting",
      "title": "Plot gene relevance or differential map",
      "topics": [
        "Gene Relevance plotting",
        "plot,GeneRelevance,character-method",
        "plot,GeneRelevance,missing-method",
        "plot,GeneRelevance,numeric-method",
        "plot_differential_map",
        "plot_differential_map,DiffusionMap,missing-method",
        "plot_differential_map,GeneRelevance,missing-method",
        "plot_differential_map,matrix,matrix-method",
        "plot_gene_relevance",
        "plot_gene_relevance,DiffusionMap,missing-method",
        "plot_gene_relevance,GeneRelevance,missing-method",
        "plot_gene_relevance,matrix,matrix-method",
        "plot_gene_relevance_rank",
        "plot_gene_relevance_rank,DiffusionMap,missing-method",
        "plot_gene_relevance_rank,GeneRelevance,missing-method",
        "plot_gene_relevance_rank,matrix,matrix-method"
      ]
    },
    {
      "page": "plot.DiffusionMap",
      "title": "3D or 2D plot of diffusion map",
      "topics": [
        "plot,DiffusionMap,missing-method",
        "plot,DiffusionMap,numeric-method",
        "plot.DiffusionMap"
      ]
    },
    {
      "page": "plot.DPT",
      "title": "Plot DPT",
      "topics": [
        "plot,DPT,missing-method",
        "plot,DPT,numeric-method",
        "plot.DPT"
      ]
    },
    {
      "page": "plot.Sigmas",
      "title": "Plot Sigmas object",
      "topics": [
        "plot,Sigmas,missing-method",
        "plot.Sigmas"
      ]
    },
    {
      "page": "projection_dist",
      "title": "Projection distance",
      "topics": [
        "projection_dist"
      ]
    },
    {
      "page": "random_root",
      "title": "Find a random root cell index",
      "topics": [
        "random_root"
      ]
    },
    {
      "page": "Sigmas-class",
      "title": "Sigmas Object",
      "topics": [
        "optimal_sigma,Sigmas-method",
        "print,Sigmas-method",
        "show,Sigmas-method",
        "Sigmas",
        "Sigmas-class",
        "Sigmas-methods"
      ]
    },
    {
      "page": "updateObject-methods",
      "title": "Update old destiny objects to a newer version.",
      "topics": [
        "updateObject methods",
        "updateObject,DiffusionMap-method",
        "updateObject,GeneRelevance-method",
        "updateObject,Sigmas-method",
        "updateObject.DiffusionMap",
        "updateObject.GeneRelevance",
        "updateObject.Sigmas"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/destiny/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "bbotk",
    "Biobase",
    "BiocGenerics",
    "boot",
    "broom",
    "car",
    "carData",
    "checkmate",
    "class",
    "cli",
    "codetools",
    "colorspace",
    "cowplot",
    "cpp11",
    "data.table",
    "DelayedArray",
    "DEoptimR",
    "Deriv",
    "digest",
    "doBy",
    "dplyr",
    "e1071",
    "evaluate",
    "farver",
    "forecast",
    "Formula",
    "fracdiff",
    "future",
    "future.apply",
    "generics",
    "GenomicRanges",
    "ggplot.multistats",
    "ggplot2",
    "ggthemes",
    "globals",
    "glue",
    "gtable",
    "hexbin",
    "IRanges",
    "irlba",
    "isoband",
    "jsonlite",
    "knn.covertree",
    "labeling",
    "laeken",
    "lattice",
    "lgr",
    "lifecycle",
    "listenv",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "mgcv",
    "minqa",
    "mirai",
    "mlbench",
    "mlr3",
    "mlr3learners",
    "mlr3measures",
    "mlr3misc",
    "mlr3pipelines",
    "mlr3tuning",
    "modelr",
    "moocore",
    "nanonext",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "palmerpenguins",
    "paradox",
    "parallelly",
    "pbkrtest",
    "pcaMethods",
    "pillar",
    "pkgconfig",
    "proxy",
    "PRROC",
    "purrr",
    "quantreg",
    "R6",
    "ranger",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppHNSW",
    "Rdpack",
    "reformulas",
    "rlang",
    "robustbase",
    "RSpectra",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "scatterplot3d",
    "Seqinfo",
    "SingleCellExperiment",
    "sp",
    "SparseArray",
    "SparseM",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "uuid",
    "vcd",
    "vctrs",
    "VIM",
    "viridisLite",
    "withr",
    "xgboost",
    "XVector",
    "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": 9.827066712600109,
  "_indexed": true,
  "_nocasepkg": "destiny",
  "_universes": [
    "bioc",
    "flying-sheep",
    "theislab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.27.0",
      "date": "2026-07-03T12:21:10.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "15c7e41670e2378b8358a2fd52fa3f7385412af5b0cf6a1e7750e9248c70ff2f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.27.0",
      "date": "2026-07-03T12:21:33.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "501f891a21f03d3d7cfd706328931809712c54dccc5f8ed332bf779c06da68e8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "3.27.0",
      "date": "2026-07-03T12:21:14.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "4235b93e336a23a1a5288e686b265d253bfe14de71f31ea6a4d9575c022a1468",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "3.27.0",
      "date": "2026-07-03T12:21:59.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "6ff50f3039d2405bc933e55ee724109dfec7f8b69e1b06ef8fb760332e8a5245",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.27.0",
      "date": "2026-07-03T12:22:01.000Z",
      "arch": "aarch64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "635a2404a6448ea7a067f29269b6ba9b781667fa934a0c41ce3a0bcdecd4d5fb",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.27.0",
      "date": "2026-07-03T12:23:38.000Z",
      "arch": "x86_64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "e54b699a55f1c9074ab0f2a1fbcef365e344639d7b96fa28887a0c8d63ac22b2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "3.27.0",
      "date": "2026-07-03T12:20:58.000Z",
      "arch": "aarch64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "e59e4fbc431986882bdeaa838a001e6293f9a2a47a7662a96de124a185bd1608",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "3.27.0",
      "date": "2026-07-03T12:23:21.000Z",
      "arch": "x86_64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "5219f4bf40c334b438153023e426eb9fbb3a6f512dd7f662621d2a4d17aef9f5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.27.0",
      "date": "2026-07-03T12:21:42.000Z",
      "arch": "emscripten",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "a6f36563da19efcd3052321915d73f258ea6542dbda0da8f4694336b33746de7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.27.0",
      "date": "2026-07-03T12:40:20.000Z",
      "arch": "x86_64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "4cea6f4b01488aaf86e7cd84b003ac538aa62a55b255efd0058942fc17916aff",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.27.0",
      "date": "2026-07-03T12:39:41.000Z",
      "arch": "x86_64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "3d335924dfbc632bd03986ccaded5372bacea9b27497daf420c07c6e9a2b1293",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "3.27.0",
      "date": "2026-07-03T12:39:09.000Z",
      "arch": "x86_64",
      "commit": "75588a3895b4d669da71f7159eb26c93dc3c04d8",
      "fileid": "c9150c23dbcfac59afdb6a5349b4a0a2cca9e8bdfc94575a1aa5e88afc52966a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28659594296"
    }
  ]
}