{
  "_id": "6ac212a0773a0037682c16c2",
  "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": "2026-10-04 08:18:18 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "ncGTW_1.27.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/937508766fb983184575f08da813339840ab9b43c6f9d73bdd66399122d3c28e",
  "_filesize": 2228778,
  "_sha256": "937508766fb983184575f08da813339840ab9b43c6f9d73bdd66399122d3c28e",
  "_expires": "2027-01-12T08:47:26.000Z",
  "_created": "2026-10-04T08:18:18.000Z",
  "_published": "2026-10-04T08:47:28.383Z",
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 12
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529",
  "_status": "success",
  "_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": "resolute",
  "_jobs": [
    {
      "job": 111395674988,
      "time": 218,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11297694193"
    },
    {
      "job": 111395675094,
      "time": 434,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11297583056"
    },
    {
      "job": 111395675089,
      "time": 673,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11297992659"
    },
    {
      "job": 111395675166,
      "time": 464,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11298412254"
    },
    {
      "job": 111395675078,
      "time": 631,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11298293506"
    },
    {
      "job": 111395675052,
      "time": 409,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11298501251"
    },
    {
      "job": 111395675037,
      "time": 960,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11298655182"
    },
    {
      "job": 111395675029,
      "time": 706,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11298775835"
    },
    {
      "job": 111395675039,
      "time": 807,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11298044642"
    },
    {
      "job": 111394448153,
      "time": 449,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11297928236"
    },
    {
      "job": 111395675001,
      "time": 174,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11297674063"
    },
    {
      "job": 111395675173,
      "time": 535,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11298243462"
    },
    {
      "job": 111395675140,
      "time": 561,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11297393662"
    },
    {
      "job": 111395675158,
      "time": 518,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11298113709"
    },
    {
      "job": 111395675160,
      "time": 543,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11298053871"
    },
    {
      "job": 111395675103,
      "time": 528,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11297744438"
    }
  ],
  "_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",
    "followers": 470,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 378,
    "source": "https://www.bioconductor.org/packages/stats/bioc/ncGTW"
  },
  "_devurl": "https://github.com/chiungtingwu/ncgtw",
  "_searchresults": 12,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/ncGTW.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_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",
    "Chromatograms",
    "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": "16-20260322-1ubuntu1",
      "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": 4.982271233039569,
  "_indexed": true,
  "_nocasepkg": "ncgtw",
  "_universes": [
    "bioc",
    "chiungtingwu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-10-04T08:21:50.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/c60ad06d0a6175fa1529a6222ab08a58297e7d6933b9f8b2640a4596639c5b72",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-10-04T08:23:37.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/9f2fa707ac4969071a6ef250470de94a4acc32c26bbecebe5fad495fc84f9151",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-10-04T08:22:32.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/8118eeb95ace031afcb6a542577c1179d53fda05b74de454612cb7fe98bc54d4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-10-04T08:23:15.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/ff65525cf1162bbf1d061a791aedebf3eb1dda849c7f64d7d3a1bf4a2d0f4e1b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-10-04T08:36:29.000Z",
      "arch": "aarch64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/b6bd006b2953328ae20605e9d2aad5cec4276b4fea1cc7f481f242e49d15834f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-10-04T08:25:28.000Z",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/91c7a80ccd419e8606b49c994737ff453ab48713a18c49875c5b8e65f562e1f3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-10-04T08:37:18.000Z",
      "arch": "aarch64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/c9ce2abe69bc4c7e68099d0a4c5a3fdcfacb8cad044b2bed779270a6e4de39a3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-10-04T08:25:25.000Z",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/1d07a069aaa94beebda4c957ad8cc500cc2238a14f30bb2c7111a3f1c29a2db5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.27.0",
      "date": "2026-10-04T08:22:05.000Z",
      "arch": "emscripten",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/139c1b865568ed30521c089178046c78bcc969df5b30905edc84c7e1ae8fecbe",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-10-04T08:22:35.000Z",
      "arch": "aarch64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/66415bd8537938e88f36fc931feb93ea7ea6b0bd91c8ab96d1df1068a79b7cb7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-10-04T08:20:41.000Z",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/7caf6c0daa2d954e1d90c1dd1893423fe088ccee95cc70fd8c56bd5169e36cd8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-10-04T08:21:01.000Z",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/25a9616a37d8229d13f97c0e726e70651afca2dc7254c30f34be209bbee7788a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-10-04T08:23:00.000Z",
      "arch": "aarch64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/664260c24e1f3d8e00b2dbd5234f91c70118da5070829906459f31865281306b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-10-04T08:20:50.000Z",
      "arch": "x86_64",
      "commit": "87c9be45d45cc6e23d1867243e3fbe8263b2f240",
      "fileid": "https://r2.ropensci.org/5e7925eceb37f4949ed7cc36d1a9e445f340f6375a7cccc634283e442acbf77e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/37188128529"
    }
  ]
}