{
  "_id": "6aca3e21fe5cc25786e85c67",
  "Package": "Fancy",
  "Type": "Package",
  "Title": "Frequency and Nonlinear Correlation Hybrid Network Inference",
  "Version": "0.99.4",
  "Authors@R": "person(\ngiven = \"Wanxin\",\nfamily = \"Lai\",\nrole = c(\"aut\", \"cre\"),\nemail = \"wanxin.graceca@gmail.com\",\ncomment = c(ORCID = \"0009-0000-1607-2453\"))",
  "URL": "https://github.com/wala-github/Fancy",
  "BugReports": "https://github.com/wala-github/Fancy/issues",
  "Description": "Infers microbial co-abundance networks by combining mutual\ninformation (via MRNET) and distance correlation into a single\nhybrid edge score. Bootstrap resampling provides\nfrequency-based confidence, and a weighted scoring function\nranks edges for downstream module analysis. Designed for\nmetagenome-assembled genome (MAG) count tables.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "biocViews": "NetworkInference, Network, Metagenomics, Microbiome,\nStatisticalMethod",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libgsl0-dev libicu-dev libx11-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-29 12:54:22 UTC",
  "RemoteUrl": "https://github.com/bioc/Fancy",
  "RemoteRef": "HEAD",
  "RemoteSha": "68202588006a4892aafa1a74833acc8ad9faced7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-10 13:27:12 UTC",
    "User": "root"
  },
  "Author": "Wanxin Lai [aut, cre] (ORCID: <https://orcid.org/0009-0000-1607-2453>)",
  "Maintainer": "Wanxin Lai <wanxin.graceca@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "Fancy_0.99.4.tar.gz",
  "_fileid": "https://r2.ropensci.org/ac0b8e576f342ff8a66684741048bd49f30cf22e46fdc5ba379cae2065f33766",
  "_filesize": 3028956,
  "_sha256": "ac0b8e576f342ff8a66684741048bd49f30cf22e46fdc5ba379cae2065f33766",
  "_expires": "2027-01-18T13:31:10.000Z",
  "_created": "2026-10-10T13:27:12.000Z",
  "_published": "2026-10-10T13:31:12.645Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38054797402",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_upstream": "https://github.com/bioc/Fancy",
  "_commit": {
    "id": "68202588006a4892aafa1a74833acc8ad9faced7",
    "author": "wala-github <graceca.norsk@gmail.com>",
    "committer": "wala-github <graceca.norsk@gmail.com>",
    "message": "Add FancyResult class and associated methods for hybrid network inference\n\n- Introduced the FancyResult S4 class to encapsulate results from the fancy pipeline.\n- Added documentation for FancyResult class and its slots.\n- Updated bootstrap_networks and fancy functions to use the new FancyResult class.\n- Implemented accessor methods for FancyResult slots using the `$` operator.\n- Modified export_cytoscape and plot methods to work with FancyResult objects.\n- Updated tests to validate functionality with the new class structure.\n- Improved vignettes to reflect changes in function signatures and usage.\n- Refactored code for better readability and consistency.\n",
    "time": 1782737662
  },
  "_maintainer": {
    "name": "Wanxin Lai",
    "email": "wanxin.graceca@gmail.com",
    "orcid": "0009-0000-1607-2453"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114223967715,
      "time": 136,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11672075685"
    },
    {
      "job": 114223967737,
      "time": 195,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11670936289"
    },
    {
      "job": 114223967742,
      "time": 178,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11671085916"
    },
    {
      "job": 114223967798,
      "time": 85,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11671125743"
    },
    {
      "job": 114223967744,
      "time": 136,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11671980866"
    },
    {
      "job": 114220997111,
      "time": 923,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11671016486"
    },
    {
      "job": 114223967775,
      "time": 123,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11671845436"
    },
    {
      "job": 114223967815,
      "time": 88,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11671060721"
    },
    {
      "job": 114223967807,
      "time": 82,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11671785916"
    },
    {
      "job": 114223967854,
      "time": 81,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11671250637"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "minet",
      "role": "Imports"
    },
    {
      "package": "compositions",
      "role": "Imports"
    },
    {
      "package": "energy",
      "role": "Imports"
    },
    {
      "package": "knnmi",
      "role": "Imports"
    },
    {
      "package": "snowfall",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "igraph",
      "role": "Suggests"
    },
    {
      "package": "magick",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-10",
      "n": 5
    },
    {
      "week": "2026-11",
      "n": 2
    },
    {
      "week": "2026-15",
      "n": 3
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-21",
      "n": 1
    },
    {
      "week": "2026-22",
      "n": 1
    },
    {
      "week": "2026-23",
      "n": 2
    },
    {
      "week": "2026-27",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "0.99.4",
      "bioc": "3.24",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "networkinference",
    "network",
    "metagenomics",
    "microbiome",
    "statisticalmethod"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "wala-github",
      "count": 23,
      "uuid": 153521607
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 216,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Fancy"
  },
  "_devurl": "https://github.com/wala-github/fancy",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/Fancy.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/wala-github/fancy",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bootstrap_networks",
    "clean_sample_names",
    "clr_normalize",
    "export_cytoscape",
    "fancy",
    "filter_mags",
    "find_optimal_k",
    "hybrid_score",
    "parse_count_tables",
    "parse_gtdb_taxonomy",
    "phyla_palette",
    "plot",
    "plot_k_elbow",
    "plot_network",
    "show",
    "threshold_edges"
  ],
  "_datasets": [
    {
      "name": "fancy_tiny_clr",
      "title": "Tiny example CLR-transformed abundance table",
      "object": "fancy_tiny_clr",
      "class": [
        "data.frame"
      ],
      "fields": [],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "fancy_tiny_counts",
      "title": "Tiny example count table",
      "object": "fancy_tiny_counts",
      "class": [
        "data.frame"
      ],
      "fields": [],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "fancy_tiny_coverage",
      "title": "Tiny example covered-fraction table",
      "object": "fancy_tiny_coverage",
      "class": [
        "data.frame"
      ],
      "fields": [],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "fancy_tiny_metadata",
      "title": "Tiny example sample metadata",
      "object": "fancy_tiny_metadata",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Sample",
        "Breed",
        "CH4"
      ],
      "rows": 321,
      "table": true,
      "tojson": true
    },
    {
      "name": "fancy_tiny_taxonomy",
      "title": "Tiny example GTDB taxonomy table",
      "object": "fancy_tiny_taxonomy",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Domain",
        "Phyla",
        "Class",
        "Order",
        "Family",
        "Genus",
        "Species"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "cash-FancyResult-method",
      "title": "Access FancyResult slots with '$'",
      "topics": [
        "$,FancyResult-method"
      ]
    },
    {
      "page": "bootstrap_networks",
      "title": "Bootstrap network inference",
      "topics": [
        "bootstrap_networks"
      ]
    },
    {
      "page": "clean_sample_names",
      "title": "Clean sample names from TSV column headers",
      "topics": [
        "clean_sample_names"
      ]
    },
    {
      "page": "clr_normalize",
      "title": "CLR-normalise a count table",
      "topics": [
        "clr_normalize"
      ]
    },
    {
      "page": "export_cytoscape",
      "title": "Export a fancy result for Cytoscape",
      "topics": [
        "export_cytoscape"
      ]
    },
    {
      "page": "fancy",
      "title": "Run the full Fancy hybrid network inference pipeline",
      "topics": [
        "fancy"
      ]
    },
    {
      "page": "fancy_tiny_clr",
      "title": "Tiny example CLR-transformed abundance table",
      "topics": [
        "fancy_tiny_clr"
      ]
    },
    {
      "page": "fancy_tiny_counts",
      "title": "Tiny example count table",
      "topics": [
        "fancy_tiny_counts"
      ]
    },
    {
      "page": "fancy_tiny_coverage",
      "title": "Tiny example covered-fraction table",
      "topics": [
        "fancy_tiny_coverage"
      ]
    },
    {
      "page": "fancy_tiny_metadata",
      "title": "Tiny example sample metadata",
      "topics": [
        "fancy_tiny_metadata"
      ]
    },
    {
      "page": "fancy_tiny_taxonomy",
      "title": "Tiny example GTDB taxonomy table",
      "topics": [
        "fancy_tiny_taxonomy"
      ]
    },
    {
      "page": "FancyResult-class",
      "title": "FancyResult: S4 container for Fancy pipeline output",
      "topics": [
        "FancyResult-class"
      ]
    },
    {
      "page": "filter_mags",
      "title": "Filter MAGs by coverage and prevalence",
      "topics": [
        "filter_mags"
      ]
    },
    {
      "page": "find_optimal_k",
      "title": "Find optimal k for the kNN MI estimator",
      "topics": [
        "find_optimal_k"
      ]
    },
    {
      "page": "hybrid_score",
      "title": "Compute hybrid edge score",
      "topics": [
        "hybrid_score"
      ]
    },
    {
      "page": "parse_count_tables",
      "title": "Parse per-sample TSV files into combined MAG-by-sample matrices",
      "topics": [
        "parse_count_tables"
      ]
    },
    {
      "page": "parse_gtdb_taxonomy",
      "title": "Parse a GTDB-format taxonomy file",
      "topics": [
        "parse_gtdb_taxonomy"
      ]
    },
    {
      "page": "phyla_palette",
      "title": "Assign colours to phyla",
      "topics": [
        "phyla_palette"
      ]
    },
    {
      "page": "plot_k_elbow",
      "title": "Plot elbow curve for k selection",
      "topics": [
        "plot_k_elbow"
      ]
    },
    {
      "page": "plot_network",
      "title": "Plot the co-abundance network",
      "topics": [
        "plot_network"
      ]
    },
    {
      "page": "plot-FancyResult-missing-method",
      "title": "Plot the hybrid score distribution of a FancyResult",
      "topics": [
        "plot,FancyResult,missing-method"
      ]
    },
    {
      "page": "show-FancyResult-method",
      "title": "Display a FancyResult",
      "topics": [
        "show,FancyResult-method"
      ]
    },
    {
      "page": "threshold_edges",
      "title": "Threshold scored edges",
      "topics": [
        "threshold_edges"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Fancy/raw/HEAD/README.md",
  "_rundeps": [
    "bayesm",
    "bit",
    "bit64",
    "boot",
    "cli",
    "clipr",
    "compositions",
    "cpp11",
    "crayon",
    "DEoptimR",
    "dplyr",
    "energy",
    "generics",
    "glue",
    "gsl",
    "hms",
    "infotheo",
    "knnmi",
    "lifecycle",
    "magrittr",
    "MASS",
    "minet",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "Rcpp",
    "RcppArmadillo",
    "readr",
    "rlang",
    "robustbase",
    "snow",
    "snowfall",
    "stringi",
    "stringr",
    "tensorA",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "Fancy_workflow.Rmd",
      "filename": "Fancy_workflow.html",
      "title": "Fancy: Hybrid Network Inference for Microbiome Co-Abundance Analysis",
      "author": "Wanxin Lai",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Positioning relative to existing Bioconductor packages",
        "Integration with the Bioconductor microbiome workflow",
        "Example Data",
        "Coverage distribution",
        "Metadata",
        "Preparing the Network Input",
        "Why a Hybrid Scoring Framework?",
        "Multiplicative scoring (default)",
        "Additive scoring",
        "dCor rescue (multiplicative mode)",
        "Running the Pipeline",
        "Inspecting Results",
        "Diagnostic Table for Known Nonlinear Pairs",
        "Edges Across Hybrid Score Bands",
        "Nonlinear Interactions Fancy Captured",
        "Re-thresholding",
        "Score Distribution",
        "Taxonomy Annotation",
        "Network Visualization",
        "Exporting for Cytoscape",
        "Saving Results",
        "Session Info"
      ],
      "created": "2026-03-08 21:13:05",
      "modified": "2026-06-29 12:54:22",
      "commits": 3
    }
  ],
  "_score": 4.653212513775344,
  "_indexed": true,
  "_nocasepkg": "fancy",
  "_universes": [
    "bioc",
    "wala-github"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.4",
      "date": "2026-10-10T13:30:24.000Z",
      "distro": "resolute",
      "commit": "68202588006a4892aafa1a74833acc8ad9faced7",
      "fileid": "https://r2.ropensci.org/fa709e99b51ede43587b0235141cbc7b909b85ddc81095cc4cb90c1759d20375",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054797402"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.99.4",
      "date": "2026-10-10T13:30:00.000Z",
      "distro": "resolute",
      "commit": "68202588006a4892aafa1a74833acc8ad9faced7",
      "fileid": "https://r2.ropensci.org/46992e461cf5385dad415c22690a030ce24561f030d95c145ed66878081b421d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054797402"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.4",
      "date": "2026-10-10T13:28:49.000Z",
      "commit": "68202588006a4892aafa1a74833acc8ad9faced7",
      "fileid": "https://r2.ropensci.org/27076648c356c9fcfe70295242ffdafd651fe406add30ece1b8e8489b2c732f4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054797402"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.99.4",
      "date": "2026-10-10T13:29:22.000Z",
      "commit": "68202588006a4892aafa1a74833acc8ad9faced7",
      "fileid": "https://r2.ropensci.org/6db4eb90b35a771c4dbd32329c4b07b0a25ec291bb37cdc623b8cbb4314367da",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054797402"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.4",
      "date": "2026-10-10T13:29:37.000Z",
      "commit": "68202588006a4892aafa1a74833acc8ad9faced7",
      "fileid": "https://r2.ropensci.org/7a762f66bd251d420e6620e7801d7319bcfbca880fe0bd9dd0c8a0d97ada13d4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054797402"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.4",
      "date": "2026-10-10T13:28:27.000Z",
      "commit": "68202588006a4892aafa1a74833acc8ad9faced7",
      "fileid": "https://r2.ropensci.org/97c4bfba0c7024990e5e19c4f165ce167ee54bfe63c4ce77210deb2e5655123b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054797402"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.4",
      "date": "2026-10-10T13:28:25.000Z",
      "commit": "68202588006a4892aafa1a74833acc8ad9faced7",
      "fileid": "https://r2.ropensci.org/8f9ae35b6f95db60bbd1dc6d4c02d864b119bd8925c25687a7b7235fe05fee10",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054797402"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.99.4",
      "date": "2026-10-10T13:28:23.000Z",
      "commit": "68202588006a4892aafa1a74833acc8ad9faced7",
      "fileid": "https://r2.ropensci.org/383bb17797cd07cd050e012cbef3149aa601309237c89815cd4de39fe836b23c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054797402"
    }
  ]
}