{
  "_id": "6a4a2b6a4727062d5eca5925",
  "Package": "squallms",
  "Type": "Package",
  "Title": "Speedy quality assurance via lasso labeling for LC-MS data",
  "Version": "1.7.0",
  "Authors@R": "c(\nperson(given = \"William\", family = \"Kumler\", email = \"wkumler@uw.edu\",\nrole = c(\"aut\", \"cre\", \"cph\"), comment=c(ORCID=\"0000-0002-5022-8009\"))\n)",
  "Description": "squallms is a Bioconductor R package that implements a\n\"semi-labeled\" approach to untargeted mass spectrometry data.\nIt pulls in raw data from mass-spec files to calculate several\nmetrics that are then used to label MS features in bulk as high\nor low quality. These metrics of peak quality are then passed\nto a simple logistic model that produces a fully-labeled\ndataset suitable for downstream analysis.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/wkumler/squallms",
  "BugReports": "https://github.com/wkumler/squallms/issues",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.1",
  "biocViews": "MassSpectrometry, Metabolomics, Proteomics, Lipidomics,\nShinyApps, Classification, Clustering, FeatureExtraction,\nPrincipalComponent, Regression, Preprocessing, QualityControl,\nVisualization",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:03:18 UTC",
  "RemoteUrl": "https://github.com/bioc/squallms",
  "RemoteRef": "HEAD",
  "RemoteSha": "454253cb0112ddd0576a789bfd024230084fd8b2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-08 11:00:38 UTC",
    "User": "root"
  },
  "Author": "William Kumler [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-5022-8009>)",
  "Maintainer": "William Kumler <wkumler@uw.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "squallms_1.7.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/c02a419ec684689df918d676b0532bdae6ebc89d93f147096e8fcd16a2c0718b",
  "_filesize": 2181853,
  "_sha256": "c02a419ec684689df918d676b0532bdae6ebc89d93f147096e8fcd16a2c0718b",
  "_expires": "2026-10-13T10:01:12.000Z",
  "_created": "2026-06-08T11:00:38.000Z",
  "_published": "2026-07-05T10:01:14.270Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27132890996",
  "_status": "success",
  "_upstream": "https://github.com/bioc/squallms",
  "_commit": {
    "id": "454253cb0112ddd0576a789bfd024230084fd8b2",
    "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": 1777381398
  },
  "_maintainer": {
    "name": "William Kumler",
    "email": "wkumler@uw.edu",
    "login": "wkumler",
    "orcid": "0000-0002-5022-8009",
    "description": "Data science manager and recent chemical oceanography Ph.D. graduate at the University of Washington",
    "uuid": 43116923
  },
  "_distro": "noble",
  "_jobs": [
    {
      "job": 85212984086,
      "time": 234,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7478410654"
    },
    {
      "job": 85212984106,
      "time": 538,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7478513887"
    },
    {
      "job": 85212984123,
      "time": 606,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7478537082"
    },
    {
      "job": 85212984117,
      "time": 299,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7478431975"
    },
    {
      "job": 85212984126,
      "time": 323,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7478440090"
    },
    {
      "job": 85212983819,
      "time": 353,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7478332034"
    },
    {
      "job": 85212984105,
      "time": 189,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7478395143"
    },
    {
      "job": 85212983807,
      "time": 485,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7478495757"
    },
    {
      "job": 85212983938,
      "time": 564,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7478523272"
    },
    {
      "job": 85212983931,
      "time": 483,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7478494312"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "xcms",
      "role": "Imports"
    },
    {
      "package": "MSnbase",
      "role": "Imports"
    },
    {
      "package": "MsExperiment",
      "role": "Imports"
    },
    {
      "package": "RaMS",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "caret",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "keys",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.7.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.6.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "massspectrometry",
    "metabolomics",
    "proteomics",
    "lipidomics",
    "shinyapps",
    "classification",
    "clustering",
    "featureextraction",
    "principalcomponent",
    "regression",
    "preprocessing",
    "qualitycontrol",
    "visualization"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "wkumler",
      "count": 131,
      "uuid": 43116923
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 235,
    "source": "https://www.bioconductor.org/packages/stats/bioc/squallms"
  },
  "_devurl": "https://github.com/wkumler/squallms",
  "_searchresults": 7,
  "_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/readme.html",
    "extra/readme.md",
    "extra/squallms.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/wkumler/squallms",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "extractChromMetrics",
    "labelFeatsLasso",
    "labelFeatsManual",
    "logModelFeatProb",
    "logModelFeatQuality",
    "makeXcmsObjFlat",
    "pickyPCA",
    "updateXcmsObjFeats"
  ],
  "_help": [
    {
      "page": "extractChromMetrics",
      "title": "Extract metrics of chromatographic peak quality",
      "topics": [
        "extractChromMetrics"
      ]
    },
    {
      "page": "labelFeatsLasso",
      "title": "Label similar chromatographic features in bulk via interactive selection",
      "topics": [
        "labelFeatsLasso"
      ]
    },
    {
      "page": "labelFeatsManual",
      "title": "Label chromatographic features manually one at a time via interactive interface",
      "topics": [
        "labelFeatsManual"
      ]
    },
    {
      "page": "logModelFeatProb",
      "title": "Model feature quality using a logistic regression",
      "topics": [
        "logModelFeatProb"
      ]
    },
    {
      "page": "logModelFeatQuality",
      "title": "Turn 0-1 likelihood values into categorical (good/bad) classifications",
      "topics": [
        "logModelFeatQuality"
      ]
    },
    {
      "page": "makeXcmsObjFlat",
      "title": "Make an XCMS object flat",
      "topics": [
        "makeXcmsObjFlat"
      ]
    },
    {
      "page": "pickyPCA",
      "title": "Perform a PCA on multi-file chromatographic data",
      "topics": [
        "pickyPCA"
      ]
    },
    {
      "page": "updateXcmsObjFeats",
      "title": "Update features in an XCMS object",
      "topics": [
        "updateXcmsObjFeats"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/squallms/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "affy",
    "affyio",
    "AnnotationFilter",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "bslib",
    "cachem",
    "caret",
    "class",
    "cli",
    "clock",
    "clue",
    "cluster",
    "codetools",
    "commonmark",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "diagram",
    "digest",
    "dir.expiry",
    "doParallel",
    "dplyr",
    "e1071",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "future",
    "future.apply",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "globals",
    "glue",
    "gower",
    "gtable",
    "hardhat",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "igraph",
    "impute",
    "ipred",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "keys",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lava",
    "lazyeval",
    "lifecycle",
    "limma",
    "listenv",
    "lubridate",
    "magrittr",
    "MALDIquant",
    "MASS",
    "MassSpecWavelet",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "MetaboCoreUtils",
    "mime",
    "ModelMetrics",
    "MsCoreUtils",
    "MsExperiment",
    "MsFeatures",
    "MSnbase",
    "MultiAssayExperiment",
    "mzID",
    "mzR",
    "ncdf4",
    "nlme",
    "nnet",
    "numDeriv",
    "openssl",
    "otel",
    "parallelly",
    "pcaMethods",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "preprocessCore",
    "prettyunits",
    "pROC",
    "prodlim",
    "progress",
    "progressr",
    "promises",
    "ProtGenerics",
    "proxy",
    "PSMatch",
    "PTMods",
    "purrr",
    "QFeatures",
    "R6",
    "RaMS",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "recipes",
    "reshape2",
    "Rhdf5lib",
    "rlang",
    "rmarkdown",
    "rpart",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shape",
    "shiny",
    "snow",
    "sourcetools",
    "SparseArray",
    "sparsevctrs",
    "Spectra",
    "SQUAREM",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "timeDate",
    "tinytex",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vsn",
    "withr",
    "xcms",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "intro_to_squallms.Rmd",
      "filename": "intro_to_squallms.html",
      "title": "Introduction to squallms",
      "author": "William Kumler",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup",
        "Installation",
        "Introduction",
        "Peakpicking with XCMS",
        "Calculating metrics of peak quality (extractChromMetrics)",
        "Labeling",
        "Manual labeling with labelFeatsManual",
        "Lasso labeling with labelFeatsLasso",
        "Building a quality model and removing low-quality peaks",
        "Vignette diagnostics"
      ],
      "created": "2024-03-27 19:08:36",
      "modified": "2024-06-07 20:35:28",
      "commits": 22
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "squallms",
  "_universes": [
    "bioc",
    "wkumler"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-06-08T11:05:06.000Z",
      "distro": "noble",
      "commit": "454253cb0112ddd0576a789bfd024230084fd8b2",
      "fileid": "https://r2.ropensci.org/6ac82781670e1965e6511dde12ebabd970fbbacc07dbd1fa5098dc19635032af",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27132890996"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-06-08T11:05:27.000Z",
      "distro": "noble",
      "commit": "454253cb0112ddd0576a789bfd024230084fd8b2",
      "fileid": "https://r2.ropensci.org/753b57ff28649d954cbd2b06ebf2d9ad4951118bb97e5c59a35fad0711d811f9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27132890996"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-06-08T11:02:49.000Z",
      "commit": "454253cb0112ddd0576a789bfd024230084fd8b2",
      "fileid": "https://r2.ropensci.org/eac6e9faa875c3872b4006c8014b41e03f351a225a11284ae215c92103e5c918",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27132890996"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-06-08T11:02:45.000Z",
      "commit": "454253cb0112ddd0576a789bfd024230084fd8b2",
      "fileid": "https://r2.ropensci.org/d5bd1644462e9ab15ba064c917bd6a8df5e90d49be2f3a0ed5ec82616e758015",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27132890996"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.7.0",
      "date": "2026-06-08T11:04:31.000Z",
      "commit": "454253cb0112ddd0576a789bfd024230084fd8b2",
      "fileid": "https://r2.ropensci.org/12f4ffbcfe781b5ba90e7be2142dd79be2eced7682209c0f7a429ddf03fd9089",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27132890996"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-06-08T11:03:10.000Z",
      "commit": "454253cb0112ddd0576a789bfd024230084fd8b2",
      "fileid": "https://r2.ropensci.org/a2e9ea81a0eca0934badc17c6e2fdcb3aec8d03064aad2f3b62a689d3d1df513",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27132890996"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-06-08T11:04:24.000Z",
      "commit": "454253cb0112ddd0576a789bfd024230084fd8b2",
      "fileid": "https://r2.ropensci.org/821e243becece660245edfc8d6f0878ae73cef61c17a3d5d25b3df3a489de47f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27132890996"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-06-08T11:02:54.000Z",
      "commit": "454253cb0112ddd0576a789bfd024230084fd8b2",
      "fileid": "https://r2.ropensci.org/88f888de9714a962c03a605cb772a68e390514113a4eef599e22437bfcf59053",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/27132890996"
    }
  ]
}