{
  "_id": "6ad9b7bcdb07788da70a9f57",
  "Package": "IgAScores",
  "Title": "Score Taxon-Level IgA Binding in IgA-Seq Experiments",
  "Version": "0.1.2.9000",
  "Authors@R": "person(given = \"Matthew\",\nfamily = \"Jackson\",\nrole = c(\"aut\", \"cre\",\"cph\"),\nemail = \"mattjackson4@gmail.com\")",
  "Description": "Functions to calculate indices used to score\nimmunoglobulin A (IgA) binding of bacteria in IgA sequencing\n(IgA-Seq) experiments. This includes the original Kau and Palm\nindices and more recent methods as described in Jackson et al.\n(2020) <doi:10.1101/2020.08.19.257501>. Additionally the\npackage contains a function to simulate IgA-Seq data and an\nexample experimental data set for method testing.",
  "URL": "https://doi.org/10.1101/2020.08.19.257501",
  "VignetteBuilder": "knitr",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.1",
  "Repository": "https://microbialman.r-universe.dev",
  "Date/Publication": "2022-05-13 11:02:21 UTC",
  "RemoteUrl": "https://github.com/microbialman/igascores",
  "RemoteRef": "HEAD",
  "RemoteSha": "0e216b8280572ffbe11c1fa7b1601bb8d9ee7c7b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-22 07:10:21 UTC",
    "User": "root"
  },
  "Author": "Matthew Jackson [aut, cre, cph]",
  "Maintainer": "Matthew Jackson <mattjackson4@gmail.com>",
  "_user": "microbialman",
  "_type": "src",
  "_file": "IgAScores_0.1.2.9000.tar.gz",
  "_fileid": "https://r2.ropensci.org/c3a4671393107dee588b3d30a955a876c88a95437fbea7a5b889b30db8485a95",
  "_filesize": 154207,
  "_sha256": "c3a4671393107dee588b3d30a955a876c88a95437fbea7a5b889b30db8485a95",
  "_expires": "2027-01-30T07:14:03.000Z",
  "_created": "2026-10-22T07:10:21.000Z",
  "_published": "2026-10-22T07:14:04.838Z",
  "_upstream": "https://github.com/microbialman/igascores",
  "_status": "success",
  "_maintainer": {
    "name": "Matthew Jackson",
    "email": "mattjackson4@gmail.com",
    "login": "microbialman",
    "linkedin": "in/matt-jackson-wood-40850378",
    "description": "Personal account, mainly previous academic work, currently principal scientist in bioinformatics @ Gilead Oxford (Prev. MiroBio)",
    "uuid": 38534482
  },
  "_jobs": [
    {
      "job": 119690409358,
      "time": 92,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12407952982"
    },
    {
      "job": 119690409387,
      "time": 99,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12408386754"
    },
    {
      "job": 119690409675,
      "time": 186,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12408357058"
    },
    {
      "job": 119690409393,
      "time": 144,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12408890070"
    },
    {
      "job": 119689507599,
      "time": 147,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12408491151"
    },
    {
      "job": 119690409469,
      "time": 66,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12408097635"
    },
    {
      "job": 119690409445,
      "time": 49,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12408741814"
    },
    {
      "job": 119690409505,
      "time": 63,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12408715553"
    },
    {
      "job": 119690409390,
      "time": 46,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12408187107"
    }
  ],
  "_buildurl": "https://github.com/r-universe/microbialman/actions/runs/39738382788",
  "_commit": {
    "id": "0e216b8280572ffbe11c1fa7b1601bb8d9ee7c7b",
    "author": "Matt Jackson-Wood <38534482+microbialman@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README.md",
    "time": 1652439741
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    }
  ],
  "_owner": "microbialman",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "microbialman",
      "count": 5,
      "uuid": 38534482
    }
  ],
  "_userbio": {
    "uuid": 38534482,
    "type": "user",
    "name": "Matt Jackson-Wood",
    "followers": 15,
    "description": "Personal account, mainly previous academic work, currently principal scientist in bioinformatics @ Gilead Oxford (Prev. MiroBio)"
  },
  "_downloads": {
    "count": 249,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/IgAScores"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/microbialman/igascores",
  "_searchresults": 15,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/IgAScores.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/microbialman/igascores",
  "_realowner": "microbialman",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.2",
      "date": "2020-09-01"
    }
  ],
  "_exports": [
    "igaprobability",
    "igaprobabilityratio",
    "igascores",
    "kauindex",
    "palmindex",
    "relabund",
    "simulateigaseq",
    "taxnamesplit"
  ],
  "_datasets": [
    {
      "name": "oligoMeta",
      "title": "Metadata for the OligoMM12-Colitis experiment used as an example in the IgAScores package",
      "object": "oligoMeta",
      "file": "oligoMeta.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SampleID",
        "Individual",
        "Gender",
        "Group",
        "Sample",
        "Day",
        "SortFraction",
        "PercentSYBR",
        "PercentIgAneg",
        "PercentIgApos"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "oligoSpecies",
      "title": "Species level counts for the OligoMM12-Colitis experiment used as an example in the IgAScores package",
      "object": "oligoSpecies",
      "file": "oligoSpecies.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CM5colneg",
        "CM5colpos",
        "CM5colw",
        "CM6colneg",
        "CM6colpos",
        "CM6colw",
        "CM7colneg",
        "CM7colpos",
        "CM7colw",
        "CM8colneg",
        "CM8colpos",
        "CM8colw",
        "I1colneg",
        "I1colpos",
        "I1colw",
        "I2colneg",
        "I2colpos",
        "I2colw",
        "I3colneg",
        "I3colpos",
        "I3colw",
        "I4colneg",
        "I4colpos",
        "I4colw",
        "NegCtrlQiagen"
      ],
      "rows": 178,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "igaprobability",
      "title": "IgA Probability",
      "topics": [
        "igaprobability"
      ]
    },
    {
      "page": "igaprobabilityratio",
      "title": "IgA Probability Ratio",
      "topics": [
        "igaprobabilityratio"
      ]
    },
    {
      "page": "igascores",
      "title": "Generate various scores for IgA binding in IgA-Seq experiments",
      "topics": [
        "igascores"
      ]
    },
    {
      "page": "kauindex",
      "title": "Kau Index",
      "topics": [
        "kauindex"
      ]
    },
    {
      "page": "oligoMeta",
      "title": "Metadata for the OligoMM12-Colitis experiment used as an example in the IgAScores package",
      "topics": [
        "oligoMeta"
      ]
    },
    {
      "page": "oligoSpecies",
      "title": "Species level counts for the OligoMM12-Colitis experiment used as an example in the IgAScores package",
      "topics": [
        "oligoSpecies"
      ]
    },
    {
      "page": "palmindex",
      "title": "Palm Index",
      "topics": [
        "palmindex"
      ]
    },
    {
      "page": "relabund",
      "title": "Relative Abundance from Counts",
      "topics": [
        "relabund"
      ]
    },
    {
      "page": "simulateigaseq",
      "title": "Simulate an IgA-Seq dataset from a pre-defined set of IgA-binding probabilities",
      "topics": [
        "simulateigaseq"
      ]
    },
    {
      "page": "taxnamesplit",
      "title": "Extract name at a given taxonomic level from a full name in the \"p__;c__;o__;f__;g__;s__\" format",
      "topics": [
        "taxnamesplit"
      ]
    }
  ],
  "_readme": "https://github.com/microbialman/igascores/raw/HEAD/README.md",
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "IgAScores.Rmd",
      "filename": "IgAScores.html",
      "title": "The IgAScores Package",
      "author": "Matthew Jackson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Input data",
        "Example data",
        "Calculating scores for all taxa and samples in an experiment",
        "Calculating scores for a single taxon from a single sample",
        "Simulating IgA-Seq data",
        "Additional examples"
      ],
      "created": "2020-08-07 15:04:01",
      "modified": "2020-08-21 09:35:23",
      "commits": 2
    }
  ],
  "_score": 4.352182518111363,
  "_indexed": true,
  "_nocasepkg": "igascores",
  "_universes": [
    "microbialman"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.2.9000",
      "date": "2026-10-22T07:11:55.000Z",
      "distro": "resolute",
      "commit": "0e216b8280572ffbe11c1fa7b1601bb8d9ee7c7b",
      "fileid": "https://r2.ropensci.org/b4861ca1256a9b1f72545b882b570b5364f0c2a24ffd9b02301eb437cdebaa59",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/microbialman/actions/runs/39738382788"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.2.9000",
      "date": "2026-10-22T07:12:04.000Z",
      "distro": "resolute",
      "commit": "0e216b8280572ffbe11c1fa7b1601bb8d9ee7c7b",
      "fileid": "https://r2.ropensci.org/7e696a7ddd7d46901655a1fd638d1e395883ebb354788c03de55ca6c3c1aa8d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/microbialman/actions/runs/39738382788"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.2.9000",
      "date": "2026-10-22T07:13:00.000Z",
      "commit": "0e216b8280572ffbe11c1fa7b1601bb8d9ee7c7b",
      "fileid": "https://r2.ropensci.org/a346497d46313153fffe9a8e7f126ea7f26a15ba9d2d2300942e9455fefd2a67",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/microbialman/actions/runs/39738382788"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.2.9000",
      "date": "2026-10-22T07:12:24.000Z",
      "commit": "0e216b8280572ffbe11c1fa7b1601bb8d9ee7c7b",
      "fileid": "https://r2.ropensci.org/99f5c0616bfff65d1e6c3259c20e99a4e1665817a2e826b4b5f8dc557e3bd7de",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/microbialman/actions/runs/39738382788"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.2.9000",
      "date": "2026-10-22T07:11:41.000Z",
      "commit": "0e216b8280572ffbe11c1fa7b1601bb8d9ee7c7b",
      "fileid": "https://r2.ropensci.org/5c979a77f5eaa04a9c2408773374e6622066e44c600c36092f29a9fa3d3bcc4a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/microbialman/actions/runs/39738382788"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.2.9000",
      "date": "2026-10-22T07:11:11.000Z",
      "commit": "0e216b8280572ffbe11c1fa7b1601bb8d9ee7c7b",
      "fileid": "https://r2.ropensci.org/d8045a8f3442844acbd685c6ffb1a59ef3a6294d1439f3e7c7c47783b045a4a5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/microbialman/actions/runs/39738382788"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.2.9000",
      "date": "2026-10-22T07:11:22.000Z",
      "commit": "0e216b8280572ffbe11c1fa7b1601bb8d9ee7c7b",
      "fileid": "https://r2.ropensci.org/1832434c8b64635b1c38f2419901a825dac21628e7e616c3f88d258481b11879",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/microbialman/actions/runs/39738382788"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.2.9000",
      "date": "2026-10-22T07:11:10.000Z",
      "commit": "0e216b8280572ffbe11c1fa7b1601bb8d9ee7c7b",
      "fileid": "https://r2.ropensci.org/3c61aa2351a59f00d0e367e6e9f93a6b72ee578c0c2fb62ab8bcc3cf1ebcce5e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/microbialman/actions/runs/39738382788"
    }
  ]
}