{
  "_id": "6a1aef3d1d7bb097a09f615a",
  "Package": "ASICS",
  "Type": "Package",
  "Title": "Automatic Statistical Identification in Complex Spectra",
  "Version": "2.29.0",
  "Authors@R": "c(\nperson(\"Gaëlle\", \"Lefort\", email = \"gaelle.lefort@inrae.fr\", role = c(\"aut\", \"cre\")),\nperson(\"Rémi\", \"Servien\", email = \"remi.servien@inrae.fr\", role = \"aut\"),\nperson(\"Patrick\", \"Tardivel\", role = \"aut\"),\nperson(\"Nathalie\", \"Vialaneix\", email = \"nathalie.vialaneix@inrae.fr\", role = \"aut\"))",
  "Description": "With a set of pure metabolite reference spectra, ASICS\nquantifies concentration of metabolites in a complex spectrum.\nThe identification of metabolites is performed by fitting a\nmixture model to the spectra of the library with a sparse\npenalty. The method and its statistical properties are\ndescribed in Tardivel et al. (2017)\n<doi:10.1007/s11306-017-1244-5>.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "Collate": "'ASICS.R' 'Spectra-class.R' 'ASICSResults-class.R'\n'AnalysisResults-class.R' 'PureLibrary-class.R' 'alignment.R'\n'analysis_on_quantification.R' 'concentration_optimisation.R'\n'data.R' 'library_transformation.R' 'load_data.R'\n'plotAlignment.R' 'plot_spectrum.R' 'simulation.R'\n'user_guide.R' 'utils.R'",
  "biocViews": "Software, DataImport, Cheminformatics, Metabolomics",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:36 UTC",
  "RemoteUrl": "https://github.com/bioc/ASICS",
  "RemoteRef": "HEAD",
  "RemoteSha": "1d197eb2eacd8e383047e9f23979f4aa09eb8e39",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:41:08 UTC",
    "User": "root"
  },
  "Author": "Gaëlle Lefort [aut, cre],\nRémi Servien [aut],\nPatrick Tardivel [aut],\nNathalie Vialaneix [aut]",
  "Maintainer": "Gaëlle Lefort <gaelle.lefort@inrae.fr>",
  "MD5sum": "2a7f4ddfdcb9df184acc01c06f7b944e",
  "_user": "bioc",
  "_type": "src",
  "_file": "ASICS_2.29.0.tar.gz",
  "_fileid": "91bc4ab2dee8957d3a3923edc2a45549b2bd8d45b2b1905d6f373699d325c668",
  "_filesize": 3921553,
  "_sha256": "91bc4ab2dee8957d3a3923edc2a45549b2bd8d45b2b1905d6f373699d325c668",
  "_created": "2026-05-30T09:41:08.000Z",
  "_published": "2026-05-30T14:07:57.933Z",
  "_jobs": [
    {
      "job": 78640330678,
      "time": 195,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307399151"
    },
    {
      "job": 78640330700,
      "time": 617,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307437583"
    },
    {
      "job": 78640330706,
      "time": 588,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307434987"
    },
    {
      "job": 78640330682,
      "time": 418,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7308743344"
    },
    {
      "job": 78640330673,
      "time": 454,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7308745410"
    },
    {
      "job": 78639580354,
      "time": 385,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307255621"
    },
    {
      "job": 78640330674,
      "time": 143,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307394163"
    },
    {
      "job": 78640330720,
      "time": 581,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307431004"
    },
    {
      "job": 78640330695,
      "time": 524,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307425722"
    },
    {
      "job": 78640330702,
      "time": 524,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307425659"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676207254",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/ASICS",
  "_commit": {
    "id": "1d197eb2eacd8e383047e9f23979f4aa09eb8e39",
    "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": 1777380456
  },
  "_maintainer": {
    "name": "Gaëlle Lefort",
    "email": "gaelle.lefort@inrae.fr"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "PepsNMR",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "quadprog",
      "role": "Imports"
    },
    {
      "package": "ropls",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "zoo",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "ASICSdata",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.29.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.28.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "dataimport",
    "cheminformatics",
    "metabolomics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 654,
    "source": "https://www.bioconductor.org/packages/stats/bioc/ASICS"
  },
  "_mentions": 10,
  "_searchresults": 31,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/ASICS.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2017-10-06"
    },
    {
      "version": "1.0.1",
      "date": "2018-01-23"
    }
  ],
  "_exports": [
    "alignSpectra",
    "ASICS",
    "ASICSUsersGuide",
    "binning",
    "createPureLibrary",
    "createSpectra",
    "formatForAnalysis",
    "getBestModel",
    "getCVError",
    "getDataset",
    "getDeformedLibrary",
    "getMeanByGroup",
    "getNbProtons",
    "getNormMethod",
    "getNormParams",
    "getPpmGrid",
    "getQuantification",
    "getReconstructedSpectra",
    "getResults",
    "getSampleName",
    "getSpectra",
    "getTypeAnalysis",
    "getTypeData",
    "importSpectra",
    "importSpectraBruker",
    "kruskalWallis",
    "normaliseSpectra",
    "oplsda",
    "pca",
    "plot",
    "plotAlignment",
    "show",
    "simulate_spectra",
    "summary"
  ],
  "_datasets": [
    {
      "name": "pure_library",
      "title": "Pure spectra library",
      "object": "sysdata",
      "class": [
        "PureLibrary"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "accessors-methods",
      "title": "Accessors",
      "topics": [
        "accessors-methods",
        "getBestModel",
        "getBestModel,AnalysisResults-method",
        "getCVError",
        "getCVError,AnalysisResults-method",
        "getDataset",
        "getDataset,AnalysisResults-method",
        "getDeformedLibrary",
        "getDeformedLibrary,ASICSResults-method",
        "getMeanByGroup",
        "getMeanByGroup,AnalysisResults-method",
        "getNbProtons",
        "getNbProtons,PureLibrary-method",
        "getNormMethod",
        "getNormMethod,Spectra-method",
        "getNormParams",
        "getNormParams,Spectra-method",
        "getPpmGrid",
        "getPpmGrid,Spectra-method",
        "getQuantification",
        "getQuantification,ASICSResults-method",
        "getReconstructedSpectra",
        "getReconstructedSpectra,ASICSResults-method",
        "getResults",
        "getResults,AnalysisResults-method",
        "getSampleName",
        "getSampleName,Spectra-method",
        "getSpectra",
        "getSpectra,Spectra-method",
        "getTypeAnalysis",
        "getTypeAnalysis,AnalysisResults-method",
        "getTypeData",
        "getTypeData,AnalysisResults-method"
      ]
    },
    {
      "page": "alignSpectra",
      "title": "Alignment",
      "topics": [
        "alignSpectra"
      ]
    },
    {
      "page": "AnalysisResults-class",
      "title": "Class AnalysisResults",
      "topics": [
        "AnalysisResults-class"
      ]
    },
    {
      "page": "ASICS",
      "title": "Automatic Statistical Identification in Complex Spectra",
      "topics": [
        "ASICS"
      ]
    },
    {
      "page": "ASICSResults-class",
      "title": "Class ASICSResults",
      "topics": [
        "ASICSResults-class"
      ]
    },
    {
      "page": "ASICSUsersGuide",
      "title": "View ASICS User's Guide",
      "topics": [
        "ASICSUsersGuide"
      ]
    },
    {
      "page": "binning",
      "title": "Binning/Bucketing of NMR spectra",
      "topics": [
        "binning"
      ]
    },
    {
      "page": "combineAndSubset-methods",
      "title": "Combine or subset functions",
      "topics": [
        "c,ASICSResults-method",
        "c,PureLibrary-method",
        "c,Spectra-method",
        "c.ASICSResults",
        "c.PureLibrary",
        "c.Spectra",
        "combineAndSubset-methods",
        "[,ASICSResults,ANY,ANY,ANY-method",
        "[,PureLibrary,ANY,ANY,ANY-method",
        "[,Spectra,ANY,ANY,ANY-method",
        "[.ASICSResults",
        "[.PureLibrary",
        "[.Spectra"
      ]
    },
    {
      "page": "createPureLibrary",
      "title": "Create a pure library",
      "topics": [
        "createPureLibrary"
      ]
    },
    {
      "page": "createSpectra",
      "title": "Create a Spectra object",
      "topics": [
        "createSpectra"
      ]
    },
    {
      "page": "formatForAnalysis",
      "title": "Format data for analysis",
      "topics": [
        "formatForAnalysis"
      ]
    },
    {
      "page": "importSpectra",
      "title": "Import metabolomic spectra",
      "topics": [
        "importSpectra"
      ]
    },
    {
      "page": "importSpectraBruker",
      "title": "Import preprocessed metabolomic spectra from Bruker files",
      "topics": [
        "importSpectraBruker"
      ]
    },
    {
      "page": "kruskalWallis",
      "title": "Kruskal-Wallis rank sum tests on a 'SummarizedExperiment' object",
      "topics": [
        "kruskalWallis"
      ]
    },
    {
      "page": "normaliseSpectra",
      "title": "Normalisation",
      "topics": [
        "normaliseSpectra"
      ]
    },
    {
      "page": "oplsda",
      "title": "Orthogonal projections to latent structures discriminant analysis (OPLS-DA) on a 'SummarizedExperiment' object",
      "topics": [
        "oplsda"
      ]
    },
    {
      "page": "pca",
      "title": "Principal Component Analysis (PCA) on a 'SummarizedExperiment' object",
      "topics": [
        "pca"
      ]
    },
    {
      "page": "plotAlignment",
      "title": "Tile plot",
      "topics": [
        "plotAlignment"
      ]
    },
    {
      "page": "pure_library",
      "title": "Pure spectra library",
      "topics": [
        "pure_library"
      ]
    },
    {
      "page": "PureLibrary-class",
      "title": "Class 'PureLibrary'",
      "topics": [
        "PureLibrary-class"
      ]
    },
    {
      "page": "simulate_spectra",
      "title": "Simulate a set of spectra",
      "topics": [
        "simulate_spectra"
      ]
    },
    {
      "page": "Spectra-class",
      "title": "Class Spectra",
      "topics": [
        "Spectra-class"
      ]
    },
    {
      "page": "summary-methods",
      "title": "Summary methods",
      "topics": [
        "dim,ASICSResults-method",
        "dim,Spectra-method",
        "dim.Spectra",
        "length,Spectra-method",
        "length.Spectra",
        "show,AnalysisResults-method",
        "show,ASICSResults-method",
        "show,Spectra-method",
        "show.AnalysisResults",
        "show.ASICSResults",
        "show.Spectra",
        "summary,AnalysisResults-method",
        "summary,Spectra-method",
        "summary-methods",
        "summary.AnalysisResults",
        "summary.Spectra"
      ]
    },
    {
      "page": "visualisation-methods-analyses",
      "title": "Visualisation methods",
      "topics": [
        "plot,AnalysisResults,ANY-method",
        "plot.AnalysisResults",
        "visualisation-methods-analyses"
      ]
    },
    {
      "page": "visualisation-methods-spectra",
      "title": "Visualisation methods",
      "topics": [
        "plot,ASICSResults,ANY-method",
        "plot,Spectra,ANY-method",
        "plot.ASICSResults",
        "plot.Spectra",
        "visualisation-methods-spectra"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocParallel",
    "bslib",
    "cachem",
    "calibrate",
    "cli",
    "codetools",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "DelayedArray",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggrepel",
    "glmnet",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "MultiAssayExperiment",
    "MultiDataSet",
    "mvtnorm",
    "openssl",
    "otel",
    "PepsNMR",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "promises",
    "ptw",
    "purrr",
    "qqman",
    "quadprog",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppDE",
    "RcppEigen",
    "reshape2",
    "rlang",
    "rmarkdown",
    "ropls",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shape",
    "snow",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "ASICS.Rmd",
      "filename": "ASICS.html",
      "title": "Automatic Statistical Identification in Complex Spectra (ASICS)",
      "author": "Gaëlle Lefort, Rémi Servien and Nathalie Vialaneix",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Package description",
        "Quick overview of main functions",
        "References"
      ],
      "created": "2017-09-28 14:24:44",
      "modified": "2020-03-20 07:54:09",
      "commits": 14
    }
  ],
  "_score": 4.792391689498254,
  "_indexed": true,
  "_nocasepkg": "asics",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.29.0",
      "date": "2026-05-30T10:06:49.000Z",
      "distro": "noble",
      "commit": "1d197eb2eacd8e383047e9f23979f4aa09eb8e39",
      "fileid": "f0d37230cf5e99872380f9f441a8ebbec467838353cd2255208b4e50a42ad3c6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676207254"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.29.0",
      "date": "2026-05-30T10:06:13.000Z",
      "distro": "noble",
      "commit": "1d197eb2eacd8e383047e9f23979f4aa09eb8e39",
      "fileid": "4747c9b30585a951451731ab1acc1a93827a78d95d70e0e22324d0c254732edb",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676207254"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.29.0",
      "date": "2026-05-30T14:01:47.000Z",
      "commit": "1d197eb2eacd8e383047e9f23979f4aa09eb8e39",
      "fileid": "166d23370c45bc97ff224481d4caceba7874ff819e766ab813468be7877b86ff",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676207254"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.29.0",
      "date": "2026-05-30T14:01:45.000Z",
      "commit": "1d197eb2eacd8e383047e9f23979f4aa09eb8e39",
      "fileid": "82f840084b039fc4c1e29bda83716b9b59e13f09decfb90b2ee501c76e1aeb84",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676207254"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.29.0",
      "date": "2026-05-30T10:05:37.000Z",
      "commit": "1d197eb2eacd8e383047e9f23979f4aa09eb8e39",
      "fileid": "b57ebcf8d5d7fa271027bbd09e7aa2cd30fed92a1d534410c3166bca9b605b45",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676207254"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.29.0",
      "date": "2026-05-30T10:05:22.000Z",
      "commit": "1d197eb2eacd8e383047e9f23979f4aa09eb8e39",
      "fileid": "cebc264af0b8643fc235c3e49145476db219c267a28f60c51c08b8edaca36cb3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676207254"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.29.0",
      "date": "2026-05-30T10:04:47.000Z",
      "commit": "1d197eb2eacd8e383047e9f23979f4aa09eb8e39",
      "fileid": "992ad3c3a56182a8a45ec9cc791840cc5943a69fbde94c9801de2da808357659",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676207254"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.29.0",
      "date": "2026-05-30T10:04:16.000Z",
      "commit": "1d197eb2eacd8e383047e9f23979f4aa09eb8e39",
      "fileid": "abae6dacbc0c6168cd52e9d3763568388a6897f4431155ff3905b8ccd6f0fc5f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676207254"
    }
  ]
}