{
  "_id": "6a1af1e51d7bb097a09f75a7",
  "Package": "ncGTW",
  "Type": "Package",
  "Title": "Alignment of LC-MS Profiles by Neighbor-wise Compound-specific\nGraphical Time Warping with Misalignment Detection",
  "Version": "1.27.0",
  "Author": "Chiung-Ting Wu <ctwu@vt.edu>",
  "Maintainer": "Chiung-Ting Wu <ctwu@vt.edu>",
  "biocViews": "Software, MassSpectrometry, Metabolomics, Alignment",
  "Description": "The purpose of ncGTW is to help XCMS for LC-MS data\nalignment. Currently, ncGTW can detect the misaligned feature\ngroups by XCMS, and the user can choose to realign these\nfeature groups by ncGTW or not.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "6.1.1",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/ChiungTingWu/ncGTW/issues",
  "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 12:50:36 UTC",
  "RemoteUrl": "https://github.com/bioc/ncGTW",
  "RemoteRef": "HEAD",
  "RemoteSha": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-30 09:42:24 UTC",
    "User": "root"
  },
  "MD5sum": "7a77186b9589cf7f2589829a958f7084",
  "_user": "bioc",
  "_type": "src",
  "_file": "ncGTW_1.27.0.tar.gz",
  "_fileid": "2e927709a850095c539ea12159d8f4026147361decca12256b2f763a0ccca9a0",
  "_filesize": 2226312,
  "_sha256": "2e927709a850095c539ea12159d8f4026147361decca12256b2f763a0ccca9a0",
  "_created": "2026-05-30T09:42:24.000Z",
  "_published": "2026-05-30T14:19:17.905Z",
  "_jobs": [
    {
      "job": 78640422862,
      "time": 234,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307427135"
    },
    {
      "job": 78640422894,
      "time": 465,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307313380"
    },
    {
      "job": 78640422890,
      "time": 734,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307472730"
    },
    {
      "job": 78640422896,
      "time": 492,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307316289"
    },
    {
      "job": 78640422888,
      "time": 662,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307466301"
    },
    {
      "job": 78640422906,
      "time": 347,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7308788656"
    },
    {
      "job": 78640422902,
      "time": 667,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307385427"
    },
    {
      "job": 78640422907,
      "time": 594,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7308813287"
    },
    {
      "job": 78640422904,
      "time": 787,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307397705"
    },
    {
      "job": 78639580478,
      "time": 488,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307266367"
    },
    {
      "job": 78640422899,
      "time": 191,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307423752"
    },
    {
      "job": 78640422898,
      "time": 537,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7307453998"
    },
    {
      "job": 78640422909,
      "time": 567,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7307456697"
    },
    {
      "job": 78640422900,
      "time": 548,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307454874"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/ncGTW",
  "_commit": {
    "id": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
    "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": 1777380636
  },
  "_maintainer": {
    "name": "Chiung-Ting Wu",
    "email": "ctwu@vt.edu",
    "login": "chiungtingwu",
    "description": "",
    "uuid": 49213701
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "BiocParallel",
      "role": "Depends"
    },
    {
      "package": "xcms",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "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": "1.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.26.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "massspectrometry",
    "metabolomics",
    "alignment",
    "cpp"
  ],
  "_stars": 8,
  "_contributors": [
    {
      "user": "chiungtingwu",
      "count": 48,
      "uuid": 49213701
    },
    {
      "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": 319,
    "source": "https://www.bioconductor.org/packages/stats/bioc/ncGTW"
  },
  "_devurl": "https://github.com/chiungtingwu/ncgtw",
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/ncGTW.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/chiungtingwu/ncgtw",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "adjustRT",
    "alignData",
    "compCV",
    "downSample",
    "groupInfo",
    "loadProfile",
    "meanCorOl",
    "misalignDetect",
    "ncGTWalign",
    "ncGTWpath",
    "ncGTWpeaks",
    "plotGroup",
    "profiles",
    "rtncGTW",
    "rtRaw",
    "scanRange"
  ],
  "_datasets": [
    {
      "name": "xcmsExamples",
      "title": "Examples of xcmsSet for inputs of ncGTW",
      "object": "xcmsExamples",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ncGTW-package",
      "title": "ncGTW: A package for detecting and aligning the misaligned features in LC-MS data",
      "topics": [
        "ncGTW-package",
        "ncGTW"
      ]
    },
    {
      "page": "adjustRT",
      "title": "Adjust retention time",
      "topics": [
        "adjustRT"
      ]
    },
    {
      "page": "ncGTWoutput-accessors",
      "title": "ncGTWoutput-accessors",
      "topics": [
        "alignData",
        "alignData,ncGTWoutput-method"
      ]
    },
    {
      "page": "compCV",
      "title": "Compare CV",
      "topics": [
        "compCV"
      ]
    },
    {
      "page": "fillPeaksChromPar",
      "title": "Edited XCMS fillPeaksChromPar for feature-wise warping functions",
      "topics": [
        "fillPeaksChromPar"
      ]
    },
    {
      "page": "getPeaksncGTW",
      "title": "Edited XCMS getPeaks for feature-wise warping functions",
      "topics": [
        "getPeaksncGTW"
      ]
    },
    {
      "page": "ncGTWinput-accessors",
      "title": "ncGTWinput-accessors",
      "topics": [
        "downSample",
        "downSample,ncGTWoutput-method",
        "groupInfo",
        "groupInfo,ncGTWinput-method",
        "ncGTWpath",
        "ncGTWpath,ncGTWoutput-method",
        "profiles",
        "profiles,ncGTWinput-method",
        "rtRaw",
        "rtRaw,ncGTWinput-method",
        "scanRange",
        "scanRange,ncGTWoutput-method"
      ]
    },
    {
      "page": "loadProfile",
      "title": "Load sample profiles for each peak group",
      "topics": [
        "loadProfile"
      ]
    },
    {
      "page": "meanCorOl",
      "title": "Compute average pairwise correlation and overlapping area",
      "topics": [
        "meanCorOl"
      ]
    },
    {
      "page": "misalignDetect",
      "title": "Detect misaligned peak groups in xcmsSet object of XCMS",
      "topics": [
        "misalignDetect"
      ]
    },
    {
      "page": "ncGTWalign",
      "title": "Run ncGTW alignment",
      "topics": [
        "ncGTWalign"
      ]
    },
    {
      "page": "ncGTWinput-class",
      "title": "Class \"ncGTWinput\"",
      "topics": [
        "ncGTWinput",
        "ncGTWinput-class"
      ]
    },
    {
      "page": "ncGTWoutput-class",
      "title": "Class \"ncGTWoutput\"",
      "topics": [
        "ncGTWoutput",
        "ncGTWoutput-class"
      ]
    },
    {
      "page": "ncGTWparam-class",
      "title": "Class \"ncGTWparam\"",
      "topics": [
        "ncGTWparam",
        "ncGTWparam-class"
      ]
    },
    {
      "page": "ncGTWwarp-class",
      "title": "Class \"ncGTWwarp\"",
      "topics": [
        "ncGTWwarp",
        "ncGTWwarp-class"
      ]
    },
    {
      "page": "plotGroup",
      "title": "Plot profiles for each peak group",
      "topics": [
        "plotGroup"
      ]
    },
    {
      "page": "ncGTWwarp-accessors",
      "title": "ncGTWwarp-accessors",
      "topics": [
        "ncGTWpeaks",
        "ncGTWpeaks,ncGTWwarp-method",
        "rtncGTW",
        "rtncGTW,ncGTWwarp-method"
      ]
    },
    {
      "page": "xcmsExamples",
      "title": "Examples of xcmsSet for inputs of ncGTW",
      "topics": [
        "xcmsExamples"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/ncGTW/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "affy",
    "affyio",
    "AnnotationFilter",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "bslib",
    "cachem",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "digest",
    "dir.expiry",
    "doParallel",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "impute",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "magrittr",
    "MALDIquant",
    "MASS",
    "MassSpecWavelet",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "MetaboCoreUtils",
    "mime",
    "MsCoreUtils",
    "MsExperiment",
    "MsFeatures",
    "MSnbase",
    "MultiAssayExperiment",
    "mzID",
    "mzR",
    "ncdf4",
    "openssl",
    "otel",
    "pcaMethods",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "preprocessCore",
    "prettyunits",
    "progress",
    "promises",
    "ProtGenerics",
    "PSMatch",
    "PTMods",
    "purrr",
    "QFeatures",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "Rhdf5lib",
    "rlang",
    "rmarkdown",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "Spectra",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "vsn",
    "withr",
    "xcms",
    "xfun",
    "XML",
    "XVector",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "ncGTW.Rmd",
      "filename": "ncGTW.html",
      "title": "ncGTW User Manual",
      "author": "Chiung-Ting Wu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Quick Start",
        "Misaligned Feature Detection and Realignment",
        "RT Structure Incorporation",
        "XCMS Preprocessing",
        "ncGTW Workflow",
        "Misaligned Feature Detection",
        "Misaligned Feature Realignment",
        "Peak-filling with Realigned RT",
        "References"
      ],
      "created": "2019-06-19 16:56:11",
      "modified": "2019-12-30 04:46:59",
      "commits": 8
    }
  ],
  "_score": 4.903089986991944,
  "_indexed": true,
  "_nocasepkg": "ncgtw",
  "_universes": [
    "bioc",
    "chiungtingwu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-30T09:46:00.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "48c9503ecef826ddee700085b03a4d2708dc1aca7d2d4a03660e4ce4f62ab5b4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-30T10:13:34.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "269a8ea54287060e2f9800456fa72ab0e9aea409acc12a7acc8a77fedf4634fd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-30T09:46:28.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "ea1ed47703c764de55c1a2407d82706a9d4f8709e18b115273ff94dcd965f9d3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-30T10:11:39.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "7e0bef30c587f67b737e05278ecd5219d2b837bf83123a265a0c343d775ddf44",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-30T14:10:54.000Z",
      "arch": "aarch64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "8fa41679c2b6529875831875ef5f44d50de4163929b6e2617ca4f3248878ec1c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-30T09:55:55.000Z",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "4597baf535474e5375ec5867b6472ed67348f0598bcb5e18f6e1dc0e9f24f626",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-30T14:11:08.000Z",
      "arch": "aarch64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "43354a79a9cc27ba61adadf80b3e1554782c2eccb9b84100b99ddb8f4cbf4222",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-30T09:57:15.000Z",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "1ab33963e2ebed4b294cfa9262e3650d1421a5129f0b02dd7289a495b6a66607",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.27.0",
      "date": "2026-05-30T10:10:49.000Z",
      "arch": "emscripten",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "f20bea10e748384d9771ccbda6844385847789534e9acf48daac24f4f69444d9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T10:09:19.000Z",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "9f4c2b445608cc36527b520e2d81479a27e5120d60f91cdaf8bf56fe4eb76173",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T10:09:01.000Z",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "2d760a57af3d81ecbeec1139c2190a36d93590ee6dc0667b38c0bfa5ef717915",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T10:09:06.000Z",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "64818ed7a72e519e90cf72ca48fdd633a0c3a8001a661a8040dbfda00e8dd477",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676156392"
    }
  ]
}