{
  "_id": "6a1ab8101d7bb097a09d5ddc",
  "Package": "qmtools",
  "Title": "Quantitative Metabolomics Data Processing Tools",
  "Version": "1.17.0",
  "Authors@R": "c(\nperson(given = \"Jaehyun\",\nfamily = \"Joo\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jaehyunjoo@outlook.com\"),\nperson(given = \"Blanca\",\nfamily = \"Himes\",\nrole = c(\"aut\"),\nemail = \"bhimes@pennmedicine.upenn.edu\")\n)",
  "Description": "The qmtools (quantitative metabolomics tools) package\nprovides basic tools for processing quantitative metabolomics\ndata with the standard SummarizedExperiment class. This\nincludes functions for imputation, normalization, feature\nfiltering, feature clustering, dimension-reduction, and\nvisualization to help users prepare data for statistical\nanalysis. This package also offers a convenient way to compute\nempirical Bayes statistics for which metabolic features are\ndifferent between two sets of study samples. Several functions\nin this package could also be used in other types of omics\ndata.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "biocViews": "Metabolomics, Preprocessing, Normalization,\nDimensionReduction, MassSpectrometry",
  "BugReports": "https://github.com/HimesGroup/qmtools/issues",
  "URL": "https://github.com/HimesGroup/qmtools",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "LazyData": "false",
  "Config/pak/sysreqs": "cmake libglpk-dev make libmagick++-dev gsfonts\nlibicu-dev libuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:09 UTC",
  "RemoteUrl": "https://github.com/bioc/qmtools",
  "RemoteRef": "HEAD",
  "RemoteSha": "d6a8cbea4122af1df8fcfd4b68e15f678e410245",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:09:30 UTC",
    "User": "root"
  },
  "Author": "Jaehyun Joo [aut, cre],\nBlanca Himes [aut]",
  "Maintainer": "Jaehyun Joo <jaehyunjoo@outlook.com>",
  "MD5sum": "387b21f944eee9105c1a7de48aee0f46",
  "_user": "bioc",
  "_type": "src",
  "_file": "qmtools_1.17.0.tar.gz",
  "_fileid": "c0a06b65d54aa62b0a9ee3bb3238021e224810323cca493ac4a7a55ee2887d9c",
  "_filesize": 1432136,
  "_sha256": "c0a06b65d54aa62b0a9ee3bb3238021e224810323cca493ac4a7a55ee2887d9c",
  "_created": "2026-05-30T07:09:30.000Z",
  "_published": "2026-05-30T10:12:32.222Z",
  "_jobs": [
    {
      "job": 78632531029,
      "time": 216,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306367883"
    },
    {
      "job": 78632531049,
      "time": 406,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306390934"
    },
    {
      "job": 78632531034,
      "time": 348,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306383862"
    },
    {
      "job": 78632531030,
      "time": 177,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307253851"
    },
    {
      "job": 78632531024,
      "time": 222,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307274692"
    },
    {
      "job": 78632259817,
      "time": 298,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306342916"
    },
    {
      "job": 78632531041,
      "time": 189,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306364559"
    },
    {
      "job": 78632531038,
      "time": 600,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306413193"
    },
    {
      "job": 78632531031,
      "time": 600,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306413146"
    },
    {
      "job": 78632531028,
      "time": 242,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306371290"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677610644",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/qmtools",
  "_commit": {
    "id": "d6a8cbea4122af1df8fcfd4b68e15f678e410245",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381089
  },
  "_maintainer": {
    "name": "Jaehyun Joo",
    "email": "jaehyunjoo@outlook.com",
    "login": "jaehyunjoo",
    "description": "Informatics",
    "uuid": 10162429
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "heatmaply",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "MsCoreUtils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "VIM",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "Rtsne",
      "role": "Suggests"
    },
    {
      "package": "missForest",
      "role": "Suggests"
    },
    {
      "package": "vsn",
      "role": "Suggests"
    },
    {
      "package": "pcaMethods",
      "role": "Suggests"
    },
    {
      "package": "pls",
      "role": "Suggests"
    },
    {
      "package": "MsFeatures",
      "role": "Suggests"
    },
    {
      "package": "impute",
      "role": "Suggests"
    },
    {
      "package": "imputeLCMD",
      "role": "Suggests"
    },
    {
      "package": "nlme",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.17.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.16.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "metabolomics",
    "preprocessing",
    "normalization",
    "dimensionreduction",
    "massspectrometry"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "jaehyunjoo",
      "count": 157,
      "uuid": 10162429
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 334,
    "source": "https://www.bioconductor.org/packages/stats/bioc/qmtools"
  },
  "_devurl": "https://github.com/himesgroup/qmtools",
  "_searchresults": 13,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/qmtools.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/himesgroup/qmtools",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "clusterFeatures",
    "compareSamples",
    "imputeIntensity",
    "imputeKNN",
    "normalizeIntensity",
    "normalizePQN",
    "plotBox",
    "plotCorr",
    "plotMiss",
    "plotReduced",
    "plotRTgroup",
    "reduceFeatures",
    "reducePCA",
    "reducePLSDA",
    "reduceTSNE",
    "removeBlankRatio",
    "removeFeatures",
    "removeICC",
    "removeMiss",
    "removeRSD",
    "scaleCols",
    "scaleRows"
  ],
  "_datasets": [
    {
      "name": "faahko_se",
      "title": "FAAH knockout LC/MS data SummarizedExperiment",
      "object": "faahko_se",
      "file": "faahko_se.rda",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "clusterFeatures",
      "title": "Feature clustering",
      "topics": [
        "clusterFeatures"
      ]
    },
    {
      "page": "compareSamples",
      "title": "Sample comparison",
      "topics": [
        "compareSamples"
      ]
    },
    {
      "page": "faahko_se",
      "title": "FAAH knockout LC/MS data SummarizedExperiment",
      "topics": [
        "faahko_se"
      ]
    },
    {
      "page": "imputeIntensity",
      "title": "Imputation methods",
      "topics": [
        "imputeIntensity",
        "imputeIntensity,ANY-method",
        "imputeIntensity,SummarizedExperiment-method"
      ]
    },
    {
      "page": "imputeKNN",
      "title": "k-nearest neighbor imputation",
      "topics": [
        "imputeKNN"
      ]
    },
    {
      "page": "normalizeIntensity",
      "title": "Normalization methods",
      "topics": [
        "normalizeIntensity",
        "normalizeIntensity,ANY-method",
        "normalizeIntensity,SummarizedExperiment-method"
      ]
    },
    {
      "page": "normalizePQN",
      "title": "Probabilistic quotient normalization (PQN)",
      "topics": [
        "normalizePQN"
      ]
    },
    {
      "page": "plotBox",
      "title": "Box plot",
      "topics": [
        "plotBox"
      ]
    },
    {
      "page": "plotCorr",
      "title": "Correlation plot",
      "topics": [
        "plotCorr"
      ]
    },
    {
      "page": "plotMiss",
      "title": "Missing value plot",
      "topics": [
        "plotMiss"
      ]
    },
    {
      "page": "plotReduced",
      "title": "Score plot of dimension-reduced data",
      "topics": [
        "plotReduced"
      ]
    },
    {
      "page": "plotRTgroup",
      "title": "Helper to visualize feature grouping",
      "topics": [
        "plotRTgroup"
      ]
    },
    {
      "page": "reduceFeatures",
      "title": "Dimension reduction methods",
      "topics": [
        "reduceFeatures",
        "reduceFeatures,ANY-method",
        "reduceFeatures,SummarizedExperiment-method"
      ]
    },
    {
      "page": "reducePCA",
      "title": "Principal component analysis (PCA)",
      "topics": [
        "reducePCA"
      ]
    },
    {
      "page": "reducePLSDA",
      "title": "Partial least squares-discriminant analysis (PLS-DA)",
      "topics": [
        "reducePLSDA"
      ]
    },
    {
      "page": "reduceTSNE",
      "title": "t-distributed stochastic neighbor embedding (t-SNE)",
      "topics": [
        "reduceTSNE"
      ]
    },
    {
      "page": "removeBlankRatio",
      "title": "Feature Filtering based on QC/blank ratio",
      "topics": [
        "removeBlankRatio"
      ]
    },
    {
      "page": "removeFeatures",
      "title": "Feature Filtering methods",
      "topics": [
        "removeFeatures",
        "removeFeatures,ANY-method",
        "removeFeatures,SummarizedExperiment-method"
      ]
    },
    {
      "page": "removeICC",
      "title": "Feature Filtering based on ICC",
      "topics": [
        "removeICC"
      ]
    },
    {
      "page": "removeMiss",
      "title": "Feature filtering based on proportions of missing values",
      "topics": [
        "removeMiss"
      ]
    },
    {
      "page": "removeRSD",
      "title": "Feature Filtering based on RSD",
      "topics": [
        "removeRSD"
      ]
    },
    {
      "page": "scaleCols",
      "title": "Scale along columns (samples)",
      "topics": [
        "scaleCols"
      ]
    },
    {
      "page": "scaleRows",
      "title": "Scale along rows (features)",
      "topics": [
        "scaleRows"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/qmtools/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "assertthat",
    "backports",
    "base64enc",
    "bbotk",
    "Biobase",
    "BiocGenerics",
    "boot",
    "broom",
    "bslib",
    "ca",
    "cachem",
    "callr",
    "car",
    "carData",
    "checkmate",
    "class",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "cowplot",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "DelayedArray",
    "dendextend",
    "DEoptimR",
    "Deriv",
    "digest",
    "doBy",
    "dplyr",
    "e1071",
    "egg",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "forecast",
    "Formula",
    "fracdiff",
    "fs",
    "future",
    "future.apply",
    "gclus",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "globals",
    "glue",
    "gridExtra",
    "gtable",
    "heatmaply",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "laeken",
    "later",
    "lattice",
    "lazyeval",
    "lgr",
    "lifecycle",
    "limma",
    "listenv",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "mirai",
    "mlbench",
    "mlr3",
    "mlr3learners",
    "mlr3measures",
    "mlr3misc",
    "mlr3pipelines",
    "mlr3tuning",
    "modelr",
    "MsCoreUtils",
    "nanonext",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "otel",
    "palmerpenguins",
    "paradox",
    "parallelly",
    "patchwork",
    "pbkrtest",
    "permute",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "processx",
    "promises",
    "proxy",
    "PRROC",
    "ps",
    "purrr",
    "qap",
    "quantreg",
    "R6",
    "ranger",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "registry",
    "reshape2",
    "rlang",
    "rmarkdown",
    "robustbase",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "seriation",
    "sp",
    "SparseArray",
    "SparseM",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tinytex",
    "TSP",
    "urca",
    "utf8",
    "uuid",
    "vcd",
    "vctrs",
    "vegan",
    "VIM",
    "viridis",
    "viridisLite",
    "webshot",
    "withr",
    "xfun",
    "xgboost",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "qmtools.Rmd",
      "filename": "qmtools.html",
      "title": "Processing quantitative metabolomics data with the qmtools package",
      "author": "Jaehyun Joo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Data preparation",
        "Feature filtering",
        "Imputation",
        "Normalization",
        "Dimension-reduction",
        "Feature clustering",
        "Sample comparison",
        "References",
        "Session info"
      ],
      "created": "2022-03-17 21:57:00",
      "modified": "2023-04-02 21:16:04",
      "commits": 4
    }
  ],
  "_score": 4.7160033436347994,
  "_indexed": true,
  "_nocasepkg": "qmtools",
  "_universes": [
    "bioc",
    "jaehyunjoo",
    "himesgroup"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.17.0",
      "date": "2026-05-30T07:14:11.000Z",
      "distro": "noble",
      "commit": "d6a8cbea4122af1df8fcfd4b68e15f678e410245",
      "fileid": "7300709695487ce3123ec0c900a484cb5e045371464fb11477ccec088fa7d3ea",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677610644"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.17.0",
      "date": "2026-05-30T07:13:13.000Z",
      "distro": "noble",
      "commit": "d6a8cbea4122af1df8fcfd4b68e15f678e410245",
      "fileid": "cf0d0cb5f3a5dba8764e0740afd2f1eeedb1870b53020989c36092cb4a269076",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677610644"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.17.0",
      "date": "2026-05-30T09:39:52.000Z",
      "commit": "d6a8cbea4122af1df8fcfd4b68e15f678e410245",
      "fileid": "3427fe1405b03055a92ff0402507b2ef9b4348f9ec3fe0c9c122be3d2e345506",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677610644"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.17.0",
      "date": "2026-05-30T09:42:47.000Z",
      "commit": "d6a8cbea4122af1df8fcfd4b68e15f678e410245",
      "fileid": "b5caf4155f5576edeb42375c412d6ba455eb4b20b5e3a6b3202c54d4ed7149e8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677610644"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.17.0",
      "date": "2026-05-30T07:13:13.000Z",
      "commit": "d6a8cbea4122af1df8fcfd4b68e15f678e410245",
      "fileid": "ff25187042bb683c9e691aee9bf057011c6f493eafd89b5ac0216e0f45be74e8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677610644"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-05-30T07:17:09.000Z",
      "commit": "d6a8cbea4122af1df8fcfd4b68e15f678e410245",
      "fileid": "18b2d3873220fb6af4acb0bfe4d2dac488ab33be12d5e61ef5719602c411b080",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677610644"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-05-30T07:17:22.000Z",
      "commit": "d6a8cbea4122af1df8fcfd4b68e15f678e410245",
      "fileid": "43d8d48c536b8adbb94304c55d289642279617ba329c8d89de0f81472484a2c8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677610644"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-05-30T07:11:22.000Z",
      "commit": "d6a8cbea4122af1df8fcfd4b68e15f678e410245",
      "fileid": "dba330a651c6ef835e35fdb36d2b653588905ef7b45af923898dbc4e9bafe47d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677610644"
    }
  ]
}