{
  "_id": "6aefa8bda2c425adab329f23",
  "Package": "seam",
  "Title": "Sparse Extended Analysis of Modules",
  "Version": "0.1.0",
  "Maintainer": "Marketa Barac Makarova <marketa.makarova@mail.muni.cz>",
  "Authors@R": "c(person(given = c(\"Marketa\", \"Barac\"),\nfamily = \"Makarova\",\nrole = c(\"aut\", \"cre\"),\nemail = \"marketa.makarova@mail.muni.cz\"),\nperson(given = \"Jan\",\nfamily = \"Kolacek\",\nrole = \"ctb\"))",
  "Description": "Provides tools for comparing groups using sparse principal\ncomponent analysis (SPCA). Includes functions for identifying\nand visualizing influential variables, assessing variable\nselection stability through bootstrapping, and exploring\nassociations with clinical traits. SPCA is implemented using\nthe method described in <doi:10.1198/106186006X113430>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-07 22:36:46 UTC",
    "User": "root"
  },
  "Author": "Marketa Barac Makarova [aut, cre], Jan Kolacek [ctb]",
  "URL": "https://github.com/marketa-makarova/seam",
  "BugReports": "https://github.com/marketa-makarova/seam/issues",
  "Config/roxygen2/version": "8.1.0",
  "Language": "en-US",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-11-07 21:01:42 UTC",
  "RemoteUrl": "https://github.com/cran/seam",
  "RemoteRef": "HEAD",
  "RemoteSha": "f59c58c4dc16ef951d021c1c7c2a536df2e7a173",
  "_user": "cran",
  "_type": "src",
  "_file": "seam_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/e881021d47adb80f5d0621cb54c082991475cf385fb60725637346423913a23e",
  "_filesize": 195191,
  "_sha256": "e881021d47adb80f5d0621cb54c082991475cf385fb60725637346423913a23e",
  "_expires": "2027-02-15T22:39:55.000Z",
  "_created": "2026-11-07T22:36:46.000Z",
  "_published": "2026-11-07T22:39:57.423Z",
  "_upstream": "https://github.com/cran/seam",
  "_status": "success",
  "_maintainer": {
    "name": "Marketa Barac Makarova",
    "email": "marketa.makarova@mail.muni.cz"
  },
  "_jobs": [
    {
      "job": 128550556152,
      "time": 135,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13593631586"
    },
    {
      "job": 128550556213,
      "time": 150,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13594091536"
    },
    {
      "job": 128549840192,
      "time": 181,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13594106140"
    },
    {
      "job": 128550556149,
      "time": 120,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13593682285"
    },
    {
      "job": 128550556161,
      "time": 80,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13594040801"
    },
    {
      "job": 128550556305,
      "time": 101,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13594141201"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/42421186102",
  "_commit": {
    "id": "f59c58c4dc16ef951d021c1c7c2a536df2e7a173",
    "author": "Marketa Barac Makarova <marketa.makarova@mail.muni.cz>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.0\n",
    "time": 1794085302
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "elasticnet",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-45",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.1.0",
      "date": "2026-11-07"
    }
  ],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 636,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/seam"
  },
  "_devurl": "https://github.com/marketa-makarova/seam",
  "_searchresults": 3,
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md",
    "extra/seam.html",
    "LICENSE"
  ],
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2026-11-07"
    }
  ],
  "_exports": [
    "compute_activity",
    "compute_module_trait_correlations",
    "compute_variable_trait_correlations",
    "insight_correlations_lollipop",
    "insight_correlations_reconstruct",
    "insight_correlations_sign_changes",
    "insight_weights_lollipop",
    "plot_activity_bar",
    "plot_activity_bubble",
    "plot_explained_variance",
    "plot_lambdas",
    "plot_module_heatmaps",
    "plot_module_trait_correlations",
    "plot_sparsity",
    "spca_all_modules",
    "spca_all_modules_grid"
  ],
  "_datasets": [
    {
      "name": "seam_demo",
      "title": "Simulated expression and trait data for two groups and two modules",
      "object": "seam_demo",
      "file": "seam_demo.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "compute_activity",
      "title": "Compute activity statuses of variables using SPCA",
      "topics": [
        "compute_activity"
      ]
    },
    {
      "page": "compute_module_trait_correlations",
      "title": "Compute Pearson's correlations between clinical traits and sparse or classic eigengenes",
      "topics": [
        "compute_module_trait_correlations"
      ]
    },
    {
      "page": "compute_variable_trait_correlations",
      "title": "Compute variable–trait correlations",
      "topics": [
        "compute_variable_trait_correlations"
      ]
    },
    {
      "page": "insight_correlations_lollipop",
      "title": "Lollipop plot of variable-trait correlations and SPCA-weighted correlations",
      "topics": [
        "insight_correlations_lollipop"
      ]
    },
    {
      "page": "insight_correlations_reconstruct",
      "title": "Reconstruct module-trait correlations from top contributing variables",
      "topics": [
        "insight_correlations_reconstruct"
      ]
    },
    {
      "page": "insight_correlations_sign_changes",
      "title": "Visualize variable-trait correlations and negative SPCA weights",
      "topics": [
        "insight_correlations_sign_changes"
      ]
    },
    {
      "page": "insight_weights_lollipop",
      "title": "Compare SPCA variable weights between two groups",
      "topics": [
        "insight_weights_lollipop"
      ]
    },
    {
      "page": "plot_activity_bar",
      "title": "Plot variable activity statuses as a stacked barplot",
      "topics": [
        "plot_activity_bar"
      ]
    },
    {
      "page": "plot_activity_bubble",
      "title": "Plot variable activity statuses as a bubble chart",
      "topics": [
        "plot_activity_bubble"
      ]
    },
    {
      "page": "plot_explained_variance",
      "title": "Plot explained variance in modules as a heatmap",
      "topics": [
        "plot_explained_variance"
      ]
    },
    {
      "page": "plot_lambdas",
      "title": "Plot SPCA sparsity and explained variance across different lambda values",
      "topics": [
        "plot_lambdas"
      ]
    },
    {
      "page": "plot_module_heatmaps",
      "title": "Plot module correlation heatmaps and sparsified heatmaps",
      "topics": [
        "plot_module_heatmaps"
      ]
    },
    {
      "page": "plot_module_trait_correlations",
      "title": "Plot module-trait correlations for sparse and classic eigengenes",
      "topics": [
        "plot_module_trait_correlations"
      ]
    },
    {
      "page": "plot_sparsity",
      "title": "Plot percentage of inactive variables (sparsity) across modules as a heatmap",
      "topics": [
        "plot_sparsity"
      ]
    },
    {
      "page": "seam",
      "title": "seam: Sparse Eigengene Analysis of Modules",
      "topics": [
        "seam"
      ]
    },
    {
      "page": "seam_demo",
      "title": "Simulated expression and trait data for two groups and two modules",
      "topics": [
        "seam_demo"
      ]
    },
    {
      "page": "spca_all_modules",
      "title": "Perform SPCA across groups and modules",
      "topics": [
        "spca_all_modules"
      ]
    },
    {
      "page": "spca_all_modules_grid",
      "title": "Perform SPCA across groups and modules with module-specific sparsity",
      "topics": [
        "spca_all_modules_grid"
      ]
    }
  ],
  "_readme": "https://github.com/cran/seam/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "elasticnet",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lars",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 1.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "seam",
  "_universes": [
    "cran",
    "marketa-makarova"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-11-07T22:38:43.000Z",
      "distro": "resolute",
      "commit": "f59c58c4dc16ef951d021c1c7c2a536df2e7a173",
      "fileid": "https://r2.ropensci.org/a6b12c142ed77e194b4471fe611fe8664da0af21cd5b2073a67ed9e37c4a19e4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/42421186102"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-11-07T22:38:56.000Z",
      "distro": "resolute",
      "commit": "f59c58c4dc16ef951d021c1c7c2a536df2e7a173",
      "fileid": "https://r2.ropensci.org/72849befc66328e33cc4b10d849226452212842bf12410d22636a84e3d02ff4b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/42421186102"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-11-07T22:39:03.000Z",
      "commit": "f59c58c4dc16ef951d021c1c7c2a536df2e7a173",
      "fileid": "https://r2.ropensci.org/9c361793dc6d4ffedfd4003eb2404c1119e947d4d6336fd6bb5c0a0b74ae81df",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/42421186102"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-11-07T22:37:46.000Z",
      "commit": "f59c58c4dc16ef951d021c1c7c2a536df2e7a173",
      "fileid": "https://r2.ropensci.org/dbbc820922f4447ec9f83ba5e98fbbdef9969726b08c1425de06a24ec28edc92",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/42421186102"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-11-07T22:38:13.000Z",
      "commit": "f59c58c4dc16ef951d021c1c7c2a536df2e7a173",
      "fileid": "https://r2.ropensci.org/dbec5299fd2f5d0b74281dbdc206d3654bf3a566232f74d8c154dc16ddf47c4b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/42421186102"
    }
  ]
}