{
  "_id": "6a1ed93eb401979e7340f2d3",
  "Package": "leiden",
  "Type": "Package",
  "Title": "R Implementation of Leiden Clustering Algorithm",
  "Version": "0.4.3.1",
  "Date": "2023-11-08",
  "Authors@R": "c(person(\"S. Thomas\", \"Kelly\", email = \"tomkellygenetics@gmail.com\", role = c(\"aut\", \"cre\", \"trl\")),\nperson(\"Vincent A.\", \"Traag\", email = \"v.a.traag@cwts.leidenuniv.nl\", role = c(\"com\")))",
  "Description": "Implements the 'Python leidenalg' module to be called in\nR. Enables clustering using the leiden algorithm for partition\na graph into communities. See the 'Python' repository for more\ndetails: <https://github.com/vtraag/leidenalg> Traag et al\n(2018) From Louvain to Leiden: guaranteeing well-connected\ncommunities. <arXiv:1810.08473>.",
  "License": "GPL-3 | file LICENSE",
  "URL": "https://github.com/TomKellyGenetics/leiden",
  "BugReports": "https://github.com/TomKellyGenetics/leiden/issues",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "Language": "en-US",
  "VignetteBuilder": "knitr",
  "Collate": "'find_partition.R' 'leiden.R' 'py_objects.R'",
  "Config/pak/sysreqs": "libglpk-dev libpng-dev libxml2-dev python3",
  "Repository": "https://tomkellygenetics.r-universe.dev",
  "Date/Publication": "2024-05-26 23:59:16 UTC",
  "RemoteUrl": "https://github.com/tomkellygenetics/leiden",
  "RemoteRef": "HEAD",
  "RemoteSha": "22ae49d7bbf28a8b635d2ac852be717a68d8a1c1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-20 09:30:01 UTC",
    "User": "root"
  },
  "Author": "S. Thomas Kelly [aut, cre, trl],\nVincent A. Traag [com]",
  "Maintainer": "S. Thomas Kelly <tomkellygenetics@gmail.com>",
  "MD5sum": "7b278215be7bcd5a6bd50e3bca1f1c9d",
  "_user": "tomkellygenetics",
  "_type": "src",
  "_file": "leiden_0.4.3.1.tar.gz",
  "_fileid": "4b92e2501584de302a0078be4a719a5b581a8bcba8bbe3ed0f33d5a52e29420b",
  "_filesize": 2645521,
  "_sha256": "4b92e2501584de302a0078be4a719a5b581a8bcba8bbe3ed0f33d5a52e29420b",
  "_created": "2026-05-20T09:30:01.000Z",
  "_published": "2026-06-02T13:23:10.641Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79080537379,
      "time": 186,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7106368088"
    },
    {
      "job": 79080537359,
      "time": 177,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7106364759"
    },
    {
      "job": 79080536631,
      "time": 221,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7106366028"
    },
    {
      "job": 79080537222,
      "time": 145,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7106347235"
    },
    {
      "job": 79080535818,
      "time": 209,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7106298720"
    },
    {
      "job": 79080535842,
      "time": 132,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7358886387"
    },
    {
      "job": 79080537210,
      "time": 228,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7106384152"
    },
    {
      "job": 79080537857,
      "time": 224,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7106382302"
    },
    {
      "job": 79080536894,
      "time": 260,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7106394837"
    }
  ],
  "_buildurl": "https://github.com/r-universe/tomkellygenetics/actions/runs/26153720895",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/tomkellygenetics/leiden",
  "_commit": {
    "id": "22ae49d7bbf28a8b635d2ac852be717a68d8a1c1",
    "author": "Tom Kelly <tomkellygenetics@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update dependencies check\n\nResolves https://github.com/TomKellyGenetics/leiden/issues/25",
    "time": 1716767956
  },
  "_maintainer": {
    "name": "S. Thomas Kelly",
    "email": "tomkellygenetics@gmail.com",
    "login": "tomkellygenetics",
    "linkedin": "in/tom-kelly-genetics",
    "twitter": "@tomkxy",
    "description": "Bioinformatician. Alumni @mikblacklab Otago, @minoda-lab RIKEN & @hugp-ri. The @carpentries instructor.\n\nGenomics | Health | Math | Stats | AWS Dev",
    "uuid": 5493325
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "reticulate",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "version": ">= 1.2.7",
      "role": "Imports"
    },
    {
      "package": "bipartite",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "data.table",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "graphsim",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "multiplex",
      "role": "Suggests"
    },
    {
      "package": "multinet",
      "role": "Suggests"
    },
    {
      "package": "network",
      "role": "Suggests"
    },
    {
      "package": "qpdf",
      "role": "Suggests"
    },
    {
      "package": "RColorBrewer",
      "role": "Suggests"
    },
    {
      "package": "remotes",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    }
  ],
  "_owner": "tomkellygenetics",
  "_selfowned": true,
  "_usedby": 3,
  "_updates": [],
  "_tags": [],
  "_stars": 43,
  "_contributors": [
    {
      "user": "tomkellygenetics",
      "count": 739,
      "uuid": 5493325
    },
    {
      "user": "yihui",
      "count": 2,
      "uuid": 163582
    }
  ],
  "_userbio": {
    "uuid": 5493325,
    "type": "user",
    "name": "Tom Kelly",
    "description": "Bioinformatician. Alumni @mikblacklab Otago, @minoda-lab RIKEN & @hugp-ri. The @carpentries instructor.\r\n\r\nGenomics | Health | Math | Stats | AWS Dev"
  },
  "_downloads": {
    "count": 4133,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/leiden"
  },
  "_devurl": "https://github.com/tomkellygenetics/leiden",
  "_searchresults": 253,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/leiden.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/tomkellygenetics/leiden",
  "_realowner": "tomkellygenetics",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.2.3",
      "date": "2019-02-11"
    },
    {
      "version": "0.3.0",
      "date": "2019-07-15"
    },
    {
      "version": "0.3.1",
      "date": "2019-07-23"
    },
    {
      "version": "0.3.2",
      "date": "2020-01-18"
    },
    {
      "version": "0.3.3",
      "date": "2020-02-04"
    },
    {
      "version": "0.3.4",
      "date": "2020-10-29"
    },
    {
      "version": "0.3.5",
      "date": "2020-11-09"
    },
    {
      "version": "0.3.6",
      "date": "2020-12-07"
    },
    {
      "version": "0.3.7",
      "date": "2021-01-26"
    },
    {
      "version": "0.3.8",
      "date": "2021-05-24"
    },
    {
      "version": "0.3.9",
      "date": "2021-07-27"
    },
    {
      "version": "0.3.10",
      "date": "2022-04-27"
    },
    {
      "version": "0.4.2",
      "date": "2022-05-09"
    },
    {
      "version": "0.4.3",
      "date": "2022-09-10"
    },
    {
      "version": "0.4.3.1",
      "date": "2023-11-17"
    }
  ],
  "_exports": [
    "leiden"
  ],
  "_help": [
    {
      "page": "leiden",
      "title": "Run Leiden clustering algorithm",
      "topics": [
        "leiden"
      ]
    }
  ],
  "_readme": "https://github.com/tomkellygenetics/leiden/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "glue",
    "here",
    "igraph",
    "jsonlite",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "pkgconfig",
    "png",
    "rappdirs",
    "Rcpp",
    "RcppTOML",
    "reticulate",
    "rlang",
    "rprojroot",
    "vctrs",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "benchmarking.Rmd",
      "filename": "benchmarking.html",
      "title": "Benchmarking the Leiden algorithm with R and Python",
      "author": "S. Thomas Kelly",
      "engine": "knitr::knitr",
      "headings": [
        "Benchmarking the Leiden Algorithm",
        "Clustering with the Leiden Algorithm in R",
        "Set up the python version to be called in R",
        "Python implementation",
        "Running in Python",
        "Benchmarking the Python version with reticulate",
        "R implementation",
        "Running in R via reticulate and igraph",
        "Calling python in R via reticulate",
        "Calling C in R with igraph",
        "Benchmarking the R version with reticulate",
        "Large adjacency matrices",
        "Comparing the adjacency matrix calling",
        "Benchmarking C in R with igraph",
        "Summary"
      ],
      "created": "2019-07-13 14:23:27",
      "modified": "2023-11-08 02:14:41",
      "commits": 23
    },
    {
      "source": "run_leiden.Rmd",
      "filename": "run_leiden.html",
      "title": "Running the Leiden algorithm with R on adjacency matrices",
      "author": "S. Thomas Kelly",
      "engine": "knitr::knitr",
      "headings": [
        "Clustering with the Leiden Algorithm in R",
        "Install",
        "Usage",
        "Running the Leiden algorithm in R",
        "Running Leiden with arguments passed to leidenalg",
        "Running on a Seurat Object",
        "Seurat version 2",
        "Seurat version 3 or later"
      ],
      "created": "2019-01-25 07:58:35",
      "modified": "2022-09-12 01:11:35",
      "commits": 26
    },
    {
      "source": "run_bipartite.Rmd",
      "filename": "run_bipartite.html",
      "title": "Running the Leiden algorithm with R on bipartite graphs",
      "author": "S. Thomas Kelly",
      "engine": "knitr::knitr",
      "headings": [
        "Clustering with the Leiden Algorithm on Bipartite Graphs",
        "Set up",
        "Usage",
        "Bipartite graph objects",
        "Running the Leiden algorithm in R",
        "Bipartite cost functions",
        "Resolution Parameter",
        "Maximum Community Size Parameter",
        "Equivalence of cost functions"
      ],
      "created": "2020-10-28 08:18:29",
      "modified": "2021-01-26 08:19:33",
      "commits": 6
    },
    {
      "source": "run_igraph.Rmd",
      "filename": "run_igraph.html",
      "title": "Running the Leiden algorithm with R on Graph Objects",
      "author": "S. Thomas Kelly",
      "engine": "knitr::knitr",
      "headings": [
        "Clustering with the Leiden Algorithm in R",
        "Install",
        "Usage",
        "Running the Leiden algorithm in R",
        "Running Leiden with arguments passed to leidenalg",
        "Running on a Seurat Object",
        "Seurat version 2",
        "Seurat version 3 or later"
      ],
      "created": "2019-07-13 05:17:36",
      "modified": "2021-07-27 06:26:55",
      "commits": 8
    },
    {
      "source": "run_multiplex.Rmd",
      "filename": "run_multiplex.html",
      "title": "Running the Leiden algorithm with R on multiplex graphs",
      "author": "S. Thomas Kelly",
      "engine": "knitr::knitr",
      "headings": [
        "Clustering with the Leiden Algorithm on Multiplex Graphs",
        "Set up",
        "Usage",
        "Multiplex graph objects",
        "Running the Leiden algorithm in R",
        "Fine-tuning with resolution",
        "Fine-tuning with maximum community size",
        "Multiplex cost functions"
      ],
      "created": "2020-12-06 15:19:36",
      "modified": "2023-11-08 02:14:41",
      "commits": 6
    }
  ],
  "_score": 9.005036900148475,
  "_indexed": true,
  "_nocasepkg": "leiden",
  "_universes": [
    "tomkellygenetics"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.4.3.1",
      "date": "2026-05-20T09:32:37.000Z",
      "distro": "noble",
      "commit": "22ae49d7bbf28a8b635d2ac852be717a68d8a1c1",
      "fileid": "73976e687204af5d66b79813ea67acc0f471bc732b4ca73ee55e0f5b72e04996",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tomkellygenetics/actions/runs/26153720895"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.4.3.1",
      "date": "2026-05-20T09:32:32.000Z",
      "distro": "noble",
      "commit": "22ae49d7bbf28a8b635d2ac852be717a68d8a1c1",
      "fileid": "9622c229d7169b03f47b5590ecb7ea6aa07e69f91ee8679e52a41d565af43dc0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tomkellygenetics/actions/runs/26153720895"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.4.3.1",
      "date": "2026-05-20T09:32:36.000Z",
      "commit": "22ae49d7bbf28a8b635d2ac852be717a68d8a1c1",
      "fileid": "e9dfa491519438a6c5276af4f0e9533333b75bae0e428677c62c2d217cb7f657",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tomkellygenetics/actions/runs/26153720895"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.4.3.1",
      "date": "2026-05-20T09:31:56.000Z",
      "commit": "22ae49d7bbf28a8b635d2ac852be717a68d8a1c1",
      "fileid": "a1d21d7d0457159bd4c4e7e5a1bebfd6dd88d4ea6c58dfb3f92fa28031ff3eb1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tomkellygenetics/actions/runs/26153720895"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.4.3.1",
      "date": "2026-05-20T09:31:36.000Z",
      "commit": "22ae49d7bbf28a8b635d2ac852be717a68d8a1c1",
      "fileid": "7353213fd1754c432b26843ff51b1478e51eff25f2c5b04b6a771fde2d1dbac3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tomkellygenetics/actions/runs/26153720895"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.4.3.1",
      "date": "2026-05-20T09:31:22.000Z",
      "commit": "22ae49d7bbf28a8b635d2ac852be717a68d8a1c1",
      "fileid": "71248957775fc774edc0d6aaed1c3b521874fdb84508be50f704798b2a9cef94",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tomkellygenetics/actions/runs/26153720895"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.4.3.1",
      "date": "2026-05-20T09:31:32.000Z",
      "commit": "22ae49d7bbf28a8b635d2ac852be717a68d8a1c1",
      "fileid": "5d614589eaa6f827cef41eee4396002ec62fe53d8d88ac4e5895e5445c2b5a15",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tomkellygenetics/actions/runs/26153720895"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.4.3.1",
      "date": "2026-06-02T13:22:32.000Z",
      "commit": "22ae49d7bbf28a8b635d2ac852be717a68d8a1c1",
      "fileid": "94c2de98ed8d091b32b4f93c84e12b19874d6155564aeb729759a93ca2e50228",
      "status": "success",
      "buildurl": "https://github.com/r-universe/tomkellygenetics/actions/runs/26153720895"
    }
  ]
}