{
  "_id": "6a197b6aacfb0bcc41df5d80",
  "Package": "protViz",
  "Type": "Package",
  "Title": "Visualizing and Analyzing Mass Spectrometry Related Data in\nProteomics",
  "Version": "0.7.12",
  "Authors@R": "c(person(\"Christian\", \"Panse\", email = \"cp@fgcz.ethz.ch\", role = c(\"aut\", \"cre\"), \ncomment = c(ORCID = \"0000-0003-1975-3064\")),\nperson(\"Jonas\", \"Grossmann\", email = \"jg@fgcz.ethz.ch\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-6899-9020\")),\nperson(\"Simon\", \"Barkow-Oesterreicher\", role = \"ctb\"))",
  "RcppModules": "FastaMod",
  "Description": "Helps with quality checks, visualizations and analysis of\nmass spectrometry data, coming from proteomics experiments. The\npackage is developed, tested and used at the Functional\nGenomics Center Zurich <https://fgcz.ch>. We use this package\nmainly for prototyping, teaching, and having fun with\nproteomics data. But it can also be used to do data analysis\nfor small scale data sets.",
  "License": "GPL-3",
  "URL": "https://github.com/cpanse/protViz/",
  "BugReports": "https://github.com/cpanse/protViz/issues",
  "Collate": "aa2mass.R centroid.R comet.R deisotoper.R de_novo.R findNN.R\nfragmentIon.R genMod.R iTRAQ2GroupAnalysis.R lcmsmap.R mascot.R\nmdp.R parentIonMass.R peakplot.R pepxml.R pgImporter.R pgLFQ.R\npp.R psm.R queue.R PTM_MarkerFinder.R ssrc.R zzz.R\nRcppExports.R protViz-package.R",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "NeedsCompilation": "yes",
  "Repository": "https://cpanse.r-universe.dev",
  "Date/Publication": "2025-06-03 07:14:39 UTC",
  "RemoteUrl": "https://github.com/cpanse/protviz",
  "RemoteRef": "HEAD",
  "RemoteSha": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
  "Packaged": {
    "Date": "2026-05-29 10:27:59 UTC",
    "User": "root"
  },
  "Author": "Christian Panse [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-1975-3064>),\nJonas Grossmann [aut] (ORCID: <https://orcid.org/0000-0002-6899-9020>),\nSimon Barkow-Oesterreicher [ctb]",
  "Maintainer": "Christian Panse <cp@fgcz.ethz.ch>",
  "MD5sum": "c6daf4961e75e131a5312b3e1b11a043",
  "_user": "cpanse",
  "_type": "src",
  "_file": "protViz_0.7.12.tar.gz",
  "_fileid": "56cca5b2c5d283381ed40693ede1b927b1c0b95ac08dc2868e9c4cf5842d1b9c",
  "_filesize": 3617901,
  "_sha256": "56cca5b2c5d283381ed40693ede1b927b1c0b95ac08dc2868e9c4cf5842d1b9c",
  "_created": "2026-05-29T10:27:59.000Z",
  "_published": "2026-05-29T11:41:30.957Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78483406025,
      "time": 156,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7288623984"
    },
    {
      "job": 78483406039,
      "time": 137,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7288618933"
    },
    {
      "job": 78483406084,
      "time": 131,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288617010"
    },
    {
      "job": 78483406069,
      "time": 144,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288620374"
    },
    {
      "job": 78483406065,
      "time": 93,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7289806990"
    },
    {
      "job": 78483406055,
      "time": 399,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7288679141"
    },
    {
      "job": 78483406047,
      "time": 131,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7289809337"
    },
    {
      "job": 78483406045,
      "time": 242,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288650032"
    },
    {
      "job": 78482768437,
      "time": 266,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288577370"
    },
    {
      "job": 78483406017,
      "time": 107,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288610158"
    },
    {
      "job": 78483406038,
      "time": 162,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7288625795"
    },
    {
      "job": 78483406052,
      "time": 140,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7288619711"
    },
    {
      "job": 78483406095,
      "time": 314,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288690540"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cpanse/protviz",
  "_commit": {
    "id": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
    "author": "Christian Panse <cp@fgcz.ethz.ch>",
    "committer": "Christian Panse <cp@fgcz.ethz.ch>",
    "message": "refactor decoy comp\n",
    "time": 1748934879
  },
  "_maintainer": {
    "name": "Christian Panse",
    "email": "cp@fgcz.ethz.ch",
    "login": "cpanse",
    "mastodon": "@hb9feb@fosstodon.org",
    "linkedin": "in/cpanse",
    "orcid": "0000-0003-1975-3064",
    "description": "proteome informatics; ms comp; visualization; maps; code; reproducible research\n@hb9feb@fosstodon.org",
    "uuid": 4901987
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0",
      "role": "Imports"
    },
    {
      "package": "lattice",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "xtable",
      "role": "Suggests"
    }
  ],
  "_owner": "cpanse",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-23",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "fun",
    "mass-spectrometry",
    "peptide-identification",
    "proteomics",
    "quantification",
    "visualization",
    "cpp"
  ],
  "_stars": 11,
  "_contributors": [
    {
      "user": "cpanse",
      "count": 255,
      "uuid": 4901987
    },
    {
      "user": "jjgg",
      "count": 1,
      "uuid": 4902603
    },
    {
      "user": "wolski",
      "count": 1,
      "uuid": 1926513
    }
  ],
  "_userbio": {
    "uuid": 4901987,
    "type": "user",
    "name": "Christian Panse",
    "description": "proteome informatics; ms comp; visualization; maps; code; reproducible research\r\n@hb9feb@fosstodon.org"
  },
  "_downloads": {
    "count": 386,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/protViz"
  },
  "_mentions": 4,
  "_devurl": "https://github.com/cpanse/protviz",
  "_searchresults": 72,
  "_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/protViz.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/cpanse/protviz",
  "_realowner": "cpanse",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.01",
      "date": "2012-11-15"
    },
    {
      "version": "0.1.45",
      "date": "2013-04-09"
    },
    {
      "version": "0.1.48",
      "date": "2013-04-18"
    },
    {
      "version": "0.1.75",
      "date": "2013-11-07"
    },
    {
      "version": "0.1.76",
      "date": "2013-11-11"
    },
    {
      "version": "0.1.95",
      "date": "2014-06-16"
    },
    {
      "version": "0.1.96",
      "date": "2014-06-18"
    },
    {
      "version": "0.1.97",
      "date": "2014-06-19"
    },
    {
      "version": "0.1.98",
      "date": "2014-06-25"
    },
    {
      "version": "0.2.06",
      "date": "2014-09-18"
    },
    {
      "version": "0.2.9",
      "date": "2014-09-30"
    },
    {
      "version": "0.2.15",
      "date": "2016-05-14"
    },
    {
      "version": "0.2.28",
      "date": "2017-01-30"
    },
    {
      "version": "0.2.31",
      "date": "2017-05-26"
    },
    {
      "version": "0.2.37",
      "date": "2017-10-12"
    },
    {
      "version": "0.2.45",
      "date": "2017-11-17"
    },
    {
      "version": "0.3.1",
      "date": "2018-06-22"
    },
    {
      "version": "0.4.0",
      "date": "2019-01-04"
    },
    {
      "version": "0.5.1",
      "date": "2019-11-18"
    },
    {
      "version": "0.6.0",
      "date": "2020-02-03"
    },
    {
      "version": "0.6.3",
      "date": "2020-03-01"
    },
    {
      "version": "0.6.4",
      "date": "2020-04-17"
    },
    {
      "version": "0.6.8",
      "date": "2020-05-02"
    },
    {
      "version": "0.7.0",
      "date": "2021-09-24"
    },
    {
      "version": "0.7.2",
      "date": "2022-03-16"
    },
    {
      "version": "0.7.3",
      "date": "2022-04-04"
    },
    {
      "version": "0.7.7",
      "date": "2023-02-06"
    },
    {
      "version": "0.7.9",
      "date": "2023-12-12"
    }
  ],
  "_exports": [
    "aa2mass",
    "as.data.frame.fragmentIonSet",
    "as.data.frame.mascot",
    "as.data.frame.psmSet",
    "as.psm.mascot_query",
    "as.psmSet",
    "assignPlatePosition",
    "blockRandom",
    "centroid",
    "de_novo",
    "defaultIon",
    "deisotoper",
    "Fasta",
    "findMz",
    "findMz.mascot",
    "findMz.psmSet",
    "findNN",
    "findNN_",
    "fragmentIon",
    "genMod",
    "insertSamples",
    "is.mascot",
    "is.mascot_query",
    "is.psm",
    "is.psmSet",
    "iTRAQ2GroupAnalysis",
    "lcmsmap",
    "lower_bound_",
    "mdp",
    "parentIonMass",
    "peakplot",
    "pgImporter",
    "pgLFQaov",
    "pgLFQtNpq",
    "plot.mascot",
    "plot.mascot_query",
    "plot.psm",
    "plot.psmSet",
    "ppp",
    "pps",
    "psm",
    "PTM_MarkerFinder",
    "PTM_MarkerFinder_util",
    "ssrc",
    "summary.cometdecoy",
    "summary.mascot",
    "summary.psmSet"
  ],
  "_datasets": [
    {
      "name": "AA",
      "title": "AA - amino acid table",
      "object": "AA",
      "class": [
        "data.frame"
      ],
      "fields": [
        "letter1",
        "letter3",
        "formula",
        "Monoisotopic",
        "Average"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "ADPR.annotation",
      "title": "ADP Ribosylated Peptide",
      "object": "ADPR",
      "class": [
        "data.frame"
      ],
      "fields": [
        "scanNr",
        "PepSeq",
        "mz",
        "LabelLow",
        "color"
      ],
      "rows": 171,
      "table": true,
      "tojson": true
    },
    {
      "name": "ADPR.lim",
      "title": "ADP Ribosylated Peptide",
      "object": "ADPR",
      "class": [
        "data.frame"
      ],
      "fields": [
        "scan",
        "rintensity",
        "xmin",
        "xmax"
      ],
      "rows": 7,
      "table": true,
      "tojson": true
    },
    {
      "name": "ADPR.ms2",
      "title": "ADP Ribosylated Peptide",
      "object": "ADPR",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "averagine",
      "title": "averagine - a data set conatining isotope envelopes of averagine peptides",
      "object": "averagine",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "100",
        "110",
        "120",
        "130",
        "140",
        "150",
        "160",
        "170",
        "180",
        "190",
        "200",
        "210",
        "220",
        "230",
        "240",
        "250",
        "260",
        "270",
        "280",
        "290",
        "300",
        "310",
        "320",
        "330",
        "340",
        "350",
        "360",
        "370",
        "380",
        "390",
        "400",
        "410",
        "420",
        "430",
        "440",
        "450",
        "460",
        "470",
        "480",
        "490",
        "500",
        "510",
        "520",
        "530",
        "540",
        "550",
        "560",
        "570",
        "580",
        "590",
        "600",
        "610",
        "620",
        "630",
        "640",
        "650",
        "660",
        "670",
        "680",
        "690",
        "700",
        "710",
        "720",
        "730",
        "740",
        "750",
        "760",
        "770",
        "780",
        "790",
        "800",
        "810",
        "820",
        "830",
        "840",
        "850",
        "860",
        "870",
        "880",
        "890",
        "900",
        "910",
        "920",
        "930",
        "940",
        "950",
        "960",
        "970",
        "980",
        "990",
        "1000",
        "1010",
        "1020",
        "1030",
        "1040",
        "1050",
        "1060",
        "1070",
        "1080",
        "1090",
        "1100",
        "1110",
        "1120",
        "1130",
        "1140",
        "1150",
        "1160",
        "1170",
        "1180",
        "1190",
        "1200",
        "1210",
        "1220",
        "1230",
        "1240",
        "1250",
        "1260",
        "1270",
        "1280",
        "1290",
        "1300",
        "1310",
        "1320",
        "1330",
        "1340",
        "1350",
        "1360",
        "1370",
        "1380",
        "1390",
        "1400",
        "1410",
        "1420",
        "1430",
        "1440",
        "1450",
        "1460",
        "1470",
        "1480",
        "1490",
        "1500",
        "1510",
        "1520",
        "1530",
        "1540",
        "1550",
        "1560",
        "1570",
        "1580",
        "1590",
        "1600",
        "1610",
        "1620",
        "1630",
        "1640",
        "1650",
        "1660",
        "1670",
        "1680",
        "1690",
        "1700",
        "1710",
        "1720",
        "1730",
        "1740",
        "1750",
        "1760",
        "1770",
        "1780",
        "1790",
        "1800",
        "1810",
        "1820",
        "1830",
        "1840",
        "1850",
        "1860",
        "1870",
        "1880",
        "1890",
        "1900",
        "1910",
        "1920",
        "1930",
        "1940",
        "1950",
        "1960",
        "1970",
        "1980",
        "1990",
        "2000",
        "2010",
        "2020",
        "2030",
        "2040",
        "2050",
        "2060",
        "2070",
        "2080",
        "2090",
        "2100",
        "2110",
        "2120",
        "2130",
        "2140",
        "2150",
        "2160",
        "2170",
        "2180",
        "2190",
        "2200",
        "2210",
        "2220",
        "2230",
        "2240",
        "2250",
        "2260",
        "2270",
        "2280",
        "2290",
        "2300",
        "2310",
        "2320",
        "2330",
        "2340",
        "2350",
        "2360",
        "2370",
        "2380",
        "2390",
        "2400",
        "2410",
        "2420",
        "2430",
        "2440",
        "2450",
        "2460",
        "2470",
        "2480",
        "2490",
        "2500",
        "2510",
        "2520",
        "2530",
        "2540",
        "2550",
        "2560",
        "2570",
        "2580",
        "2590",
        "2600",
        "2610",
        "2620",
        "2630",
        "2640",
        "2650",
        "2660",
        "2670",
        "2680",
        "2690",
        "2700",
        "2710",
        "2720",
        "2730",
        "2740",
        "2750",
        "2760",
        "2770",
        "2780",
        "2790",
        "2800",
        "2810",
        "2820",
        "2830",
        "2840",
        "2850",
        "2860",
        "2870",
        "2880",
        "2890",
        "2900",
        "2910",
        "2920",
        "2930",
        "2940",
        "2950",
        "2960",
        "2970",
        "2980",
        "2990",
        "3000",
        "3010",
        "3020",
        "3030",
        "3040",
        "3050",
        "3060",
        "3070",
        "3080",
        "3090",
        "3100",
        "3110",
        "3120",
        "3130",
        "3140",
        "3150",
        "3160",
        "3170",
        "3180",
        "3190",
        "3200",
        "3210",
        "3220",
        "3230",
        "3240",
        "3250",
        "3260",
        "3270",
        "3280",
        "3290",
        "3300",
        "3310",
        "3320",
        "3330",
        "3340",
        "3350",
        "3360",
        "3370",
        "3380",
        "3390",
        "3400",
        "3410",
        "3420",
        "3430",
        "3440",
        "3450",
        "3460",
        "3470",
        "3480",
        "3490",
        "3500",
        "3510",
        "3520",
        "3530",
        "3540",
        "3550",
        "3560",
        "3570",
        "3580",
        "3590",
        "3600",
        "3610",
        "3620",
        "3630",
        "3640",
        "3650",
        "3660",
        "3670",
        "3680",
        "3690",
        "3700",
        "3710",
        "3720",
        "3730",
        "3740",
        "3750",
        "3760",
        "3770",
        "3780",
        "3790",
        "3800",
        "3810",
        "3820",
        "3830",
        "3840",
        "3850",
        "3860",
        "3870",
        "3880",
        "3890",
        "3900",
        "3910",
        "3920",
        "3930",
        "3940",
        "3950",
        "3960",
        "3970",
        "3980",
        "3990",
        "4000",
        "4010",
        "4020",
        "4030",
        "4040",
        "4050",
        "4060",
        "4070",
        "4080",
        "4090",
        "4100",
        "4110",
        "4120",
        "4130",
        "4140",
        "4150",
        "4160",
        "4170",
        "4180",
        "4190",
        "4200",
        "4210",
        "4220",
        "4230",
        "4240",
        "4250",
        "4260",
        "4270",
        "4280",
        "4290",
        "4300",
        "4310",
        "4320",
        "4330",
        "4340",
        "4350",
        "4360",
        "4370",
        "4380",
        "4390",
        "4400",
        "4410",
        "4420",
        "4430",
        "4440",
        "4450",
        "4460",
        "4470",
        "4480",
        "4490",
        "4500",
        "4510",
        "4520",
        "4530",
        "4540",
        "4550",
        "4560",
        "4570",
        "4580",
        "4590",
        "4600",
        "4610",
        "4620",
        "4630",
        "4640",
        "4650",
        "4660",
        "4670",
        "4680",
        "4690",
        "4700",
        "4710",
        "4720",
        "4730",
        "4740",
        "4750",
        "4760",
        "4770",
        "4780",
        "4790",
        "4800",
        "4810",
        "4820",
        "4830",
        "4840",
        "4850",
        "4860",
        "4870",
        "4880",
        "4890",
        "4900",
        "4910",
        "4920",
        "4930",
        "4940",
        "4950",
        "4960",
        "4970",
        "4980",
        "4990",
        "5000",
        "5010",
        "5020",
        "5030",
        "5040",
        "5050",
        "5060",
        "5070",
        "5080",
        "5090",
        "5100",
        "5110",
        "5120",
        "5130",
        "5140",
        "5150",
        "5160",
        "5170",
        "5180",
        "5190",
        "5200",
        "5210",
        "5220",
        "5230",
        "5240",
        "5250",
        "5260",
        "5270",
        "5280",
        "5290",
        "5300",
        "5310",
        "5320",
        "5330",
        "5340",
        "5350",
        "5360",
        "5370",
        "5380",
        "5390",
        "5400",
        "5410",
        "5420",
        "5430",
        "5440",
        "5450",
        "5460",
        "5470",
        "5480",
        "5490",
        "5500",
        "5510",
        "5520",
        "5530",
        "5540",
        "5550",
        "5560",
        "5570",
        "5580",
        "5590",
        "5600",
        "5610",
        "5620",
        "5630",
        "5640",
        "5650",
        "5660",
        "5670",
        "5680",
        "5690",
        "5700",
        "5710",
        "5720",
        "5730",
        "5740",
        "5750",
        "5760",
        "5770",
        "5780",
        "5790",
        "5800",
        "5810",
        "5820",
        "5830",
        "5840",
        "5850",
        "5860",
        "5870",
        "5880",
        "5890",
        "5900",
        "5910",
        "5920",
        "5930",
        "5940",
        "5950",
        "5960",
        "5970",
        "5980",
        "5990",
        "6000",
        "6010",
        "6020",
        "6030",
        "6040",
        "6050",
        "6060",
        "6070",
        "6080",
        "6090",
        "6100",
        "6110",
        "6120",
        "6130",
        "6140",
        "6150",
        "6160",
        "6170",
        "6180",
        "6190",
        "6200",
        "6210",
        "6220",
        "6230",
        "6240",
        "6250",
        "6260",
        "6270",
        "6280",
        "6290",
        "6300",
        "6310",
        "6320",
        "6330",
        "6340",
        "6350",
        "6360",
        "6370",
        "6380",
        "6390",
        "6400",
        "6410",
        "6420",
        "6430",
        "6440",
        "6450",
        "6460",
        "6470",
        "6480",
        "6490",
        "6500",
        "6510",
        "6520",
        "6530",
        "6540",
        "6550",
        "6560",
        "6570",
        "6580",
        "6590",
        "6600",
        "6610",
        "6620",
        "6630",
        "6640",
        "6650",
        "6660",
        "6670",
        "6680",
        "6690",
        "6700",
        "6710",
        "6720",
        "6730",
        "6740",
        "6750",
        "6760",
        "6770",
        "6780",
        "6790",
        "6800",
        "6810",
        "6820",
        "6830",
        "6840",
        "6850",
        "6860",
        "6870",
        "6880",
        "6890",
        "6900",
        "6910",
        "6920",
        "6930",
        "6940",
        "6950",
        "6960",
        "6970",
        "6980",
        "6990",
        "7000",
        "7010",
        "7020",
        "7030",
        "7040",
        "7050",
        "7060",
        "7070",
        "7080",
        "7090",
        "7100",
        "7110",
        "7120",
        "7130",
        "7140",
        "7150",
        "7160",
        "7170",
        "7180",
        "7190",
        "7200",
        "7210",
        "7220",
        "7230",
        "7240",
        "7250",
        "7260",
        "7270",
        "7280",
        "7290",
        "7300",
        "7310",
        "7320",
        "7330",
        "7340",
        "7350",
        "7360",
        "7370",
        "7380",
        "7390",
        "7400",
        "7410",
        "7420",
        "7430",
        "7440",
        "7450",
        "7460",
        "7470",
        "7480",
        "7490",
        "7500",
        "7510",
        "7520",
        "7530",
        "7540",
        "7550",
        "7560",
        "7570",
        "7580",
        "7590",
        "7600",
        "7610",
        "7620",
        "7630",
        "7640",
        "7650",
        "7660",
        "7670",
        "7680",
        "7690",
        "7700",
        "7710",
        "7720",
        "7730",
        "7740",
        "7750",
        "7760",
        "7770",
        "7780",
        "7790",
        "7800",
        "7810",
        "7820",
        "7830",
        "7840",
        "7850",
        "7860",
        "7870",
        "7880",
        "7890",
        "7900",
        "7910",
        "7920",
        "7930",
        "7940",
        "7950",
        "7960",
        "7970",
        "7980",
        "7990",
        "8000"
      ],
      "rows": 8,
      "table": true,
      "tojson": true
    },
    {
      "name": "fetuinLFQ",
      "title": "fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.",
      "object": "fetuinLFQ",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "HexNAc",
      "title": "HexNAc - Analysis of N-HexNAc glycopeptides by LC-MS/MS, using HCD and ETD fragmentation techniques",
      "object": "HexNAc",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "iRTpeptides",
      "title": "iRT peptides - independent retention time peptides",
      "object": "iRTpeptides",
      "class": [
        "data.frame"
      ],
      "fields": [
        "peptide",
        "rt"
      ],
      "rows": 31,
      "table": true,
      "tojson": true
    },
    {
      "name": "iTRAQ",
      "title": "iTRAQ - A small 8-plex iTRAQ data set with confident identified peptides from 5 proteins.",
      "object": "iTRAQ",
      "class": [
        "data.frame"
      ],
      "fields": [
        "prot",
        "peptide",
        "area113",
        "area114",
        "area115",
        "area116",
        "area117",
        "area118",
        "area119",
        "area121",
        "desc"
      ],
      "rows": 264,
      "table": true,
      "tojson": true
    },
    {
      "name": "msms",
      "title": "A data set containing tandem mass spectra of an LCMS experiment.",
      "object": "msms",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "pgLFQfeature",
      "title": "pgLFQfeature - A data set with a featuremap export ProgenesisLCMS",
      "object": "pgLFQfeature",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "pgLFQprot",
      "title": "pgLFQprot - A data set with a featuremap export ProgenesisLCMS",
      "object": "pgLFQprot",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "pressureProfile",
      "title": "NanoLC pressure profile",
      "object": "pressureProfile",
      "class": [
        "data.frame"
      ],
      "fields": [
        "filename",
        "time",
        "Qb",
        "Pc"
      ],
      "rows": 193187,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "AA",
      "title": "AA - amino acid table",
      "topics": [
        "AA"
      ]
    },
    {
      "page": "aa2mass",
      "title": "determine the weight if a fiven amino acid sequence",
      "topics": [
        "aa2mass"
      ]
    },
    {
      "page": "ADPR",
      "title": "ADP Ribosylated Peptide",
      "topics": [
        "ADPR",
        "ADPR.annotation",
        "ADPR.lim",
        "ADPR.ms2"
      ]
    },
    {
      "page": "psmSet",
      "title": "psmSet - a set of peptide spectrum matches",
      "topics": [
        "as.psmSet",
        "as.psmSet.mascot",
        "is.psmSet"
      ]
    },
    {
      "page": "assignPlatePosition",
      "title": "Assign an instrument queue configuration to a plate",
      "topics": [
        "assignPlatePosition"
      ]
    },
    {
      "page": "averagine",
      "title": "averagine - a data set conatining isotope envelopes of averagine peptides",
      "topics": [
        "averagine"
      ]
    },
    {
      "page": "blockRandom",
      "title": "Derive a randomization of a table.",
      "topics": [
        "blockRandom"
      ]
    },
    {
      "page": "centroid",
      "title": "Centroid a spectrum acquired in profile mode",
      "topics": [
        "centroid",
        "profile"
      ]
    },
    {
      "page": "de_novo",
      "title": "de-novo on tandem ms",
      "topics": [
        "de_novo"
      ]
    },
    {
      "page": "deisotoper",
      "title": "find isotop pattern in a given mass spectrum",
      "topics": [
        "deisotoper"
      ]
    },
    {
      "page": "fasta",
      "title": "FASTA format reader",
      "topics": [
        "FASTA",
        "Fasta",
        "fasta"
      ]
    },
    {
      "page": "fetuinLFQ",
      "title": "fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.",
      "topics": [
        "apex",
        "empai",
        "fetuinLFQ",
        "t3pq"
      ]
    },
    {
      "page": "findNN",
      "title": "find index of nearest neighbor",
      "topics": [
        "findNN",
        "findNN_",
        "lower_bound_",
        "NN"
      ]
    },
    {
      "page": "fragmentIons",
      "title": "Compute the b and y Fragment Ions of a Peptide Sequence",
      "topics": [
        "as.data.frame.fragmentIonSet",
        "bymatrix",
        "defaultIon",
        "fragmentIon",
        "ionseries"
      ]
    },
    {
      "page": "genMod",
      "title": "Generates all possible modification of a given peptide seqence and modification pattern",
      "topics": [
        "genMod"
      ]
    },
    {
      "page": "HexNAc",
      "title": "HexNAc - Analysis of N-HexNAc glycopeptides by LC-MS/MS, using HCD and ETD fragmentation techniques",
      "topics": [
        "HexNAc"
      ]
    },
    {
      "page": "insertSamples",
      "title": "Insert sample on a given position",
      "topics": [
        "insertSamples"
      ]
    },
    {
      "page": "iRTpeptides",
      "title": "iRT peptides - independent retention time peptides",
      "topics": [
        "iRT",
        "irt",
        "iRTpeptides"
      ]
    },
    {
      "page": "iTRAQ",
      "title": "iTRAQ - A small 8-plex iTRAQ data set with confident identified peptides from 5 proteins.",
      "topics": [
        "iTRAQ"
      ]
    },
    {
      "page": "iTRAQ2GroupAnalysis",
      "title": "iTRAQ two group analysis",
      "topics": [
        "iTRAQ2GroupAnalysis"
      ]
    },
    {
      "page": "lcmsmap",
      "title": "LC-MS Map",
      "topics": [
        "lcmsmap",
        "lcmsoverview",
        "pep3d",
        "plot.psmSet"
      ]
    },
    {
      "page": "mascot",
      "title": "Generic methods for mascot results",
      "topics": [
        "as.data.frame.mascot",
        "as.psm.mascot_query",
        "is.mascot",
        "is.mascot_query",
        "mascot",
        "plot.mascot",
        "plot.mascot_query",
        "summary.cometdecoy",
        "summary.mascot"
      ]
    },
    {
      "page": "mdp",
      "title": "Mass Deviation Plot",
      "topics": [
        "massDeviationPlot",
        "mdp"
      ]
    },
    {
      "page": "msms",
      "title": "A data set containing tandem mass spectra of an LCMS experiment.",
      "topics": [
        "msms"
      ]
    },
    {
      "page": "parentIonMass",
      "title": "Compute Parent Ion Mass of a Peptide Sequence",
      "topics": [
        "parentIonMass",
        "pepmass",
        "pim"
      ]
    },
    {
      "page": "peakplot",
      "title": "Labelling of Peptide Fragment Mass Spectra",
      "topics": [
        "peaklist",
        "peaklistSet",
        "peakplot",
        "peakplot.label",
        "peakplot.pie",
        "peakplot.putlabel",
        "plot.psm",
        "protViz"
      ]
    },
    {
      "page": "pgImporter",
      "title": "Progenesis Importer Function",
      "topics": [
        "pgImporter"
      ]
    },
    {
      "page": "pgLFQaov",
      "title": "iTRAQ two group analysis",
      "topics": [
        "pgLFQaov"
      ]
    },
    {
      "page": "pgLFQfeature",
      "title": "pgLFQfeature - A data set with a featuremap export ProgenesisLCMS",
      "topics": [
        "pgLFQfeature"
      ]
    },
    {
      "page": "pgLFQprot",
      "title": "pgLFQprot - A data set with a featuremap export ProgenesisLCMS",
      "topics": [
        "pgLFQprot"
      ]
    },
    {
      "page": "pgLFQtNpq",
      "title": "Label Free Quantification using the top N peptide approach",
      "topics": [
        "pgLFQtNpq",
        "tNpq"
      ]
    },
    {
      "page": "pressureProfile",
      "title": "NanoLC pressure profile",
      "topics": [
        "pressureProfile"
      ]
    },
    {
      "page": "ppp",
      "title": "Plotting pressure profile data from Eksigent LC pumps",
      "topics": [
        "ppp",
        "pressureProfilePlot"
      ]
    },
    {
      "page": "pps",
      "title": "A misc function for finding NN time slots in pressure profile data.",
      "topics": [
        "pps",
        "pressureProfileSummary"
      ]
    },
    {
      "page": "psm",
      "title": "Compute a matching between a peptide sequence and a MS2 spectrum",
      "topics": [
        "as.data.frame.psmSet",
        "is.psm",
        "psm",
        "summary.psmSet"
      ]
    },
    {
      "page": "PTM_MarkerFinder",
      "title": "PTM MarkerFinder",
      "topics": [
        "findMz",
        "findMz.mascot",
        "findMz.psmSet",
        "pPTM",
        "PTM_MarkerFinder"
      ]
    },
    {
      "page": "PTM_MarkerFinder_util",
      "title": "PTM MarkerFinder util plot",
      "topics": [
        "PTM_MarkerFinder_util"
      ]
    },
    {
      "page": "ssrc",
      "title": "Sequence Specific Retention Calculator",
      "topics": [
        "hydrophobicity",
        "ssrc"
      ]
    }
  ],
  "_readme": "https://github.com/cpanse/protviz/raw/HEAD/README.md",
  "_rundeps": [
    "Rcpp"
  ],
  "_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": "ADP-Ribosylated-peptides.Rnw",
      "filename": "ADP-Ribosylated-peptides.pdf",
      "title": "ADP Ribosylated Peptides",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2022-04-04 11:37:29",
      "modified": "2022-05-25 09:19:03",
      "commits": 2
    },
    {
      "source": "PTM_MarkerFinder.Rnw",
      "filename": "PTM_MarkerFinder.pdf",
      "title": "Howto find putative ptm marker ion?",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2014-12-19 09:55:59",
      "modified": "2019-11-18 08:38:17",
      "commits": 14
    },
    {
      "source": "protViz.Rnw",
      "filename": "protViz.pdf",
      "title": "primer - protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2014-12-19 09:55:59",
      "modified": "2022-04-14 08:19:58",
      "commits": 22
    },
    {
      "source": "poster.Rnw",
      "filename": "poster.pdf",
      "title": "protViz package poster (in portrait)",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2017-06-19 08:45:06",
      "modified": "2019-01-04 07:22:13",
      "commits": 7
    }
  ],
  "_score": 7.880996414629061,
  "_indexed": true,
  "_nocasepkg": "protviz",
  "_universes": [
    "cpanse"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.7.12",
      "date": "2026-05-29T10:30:31.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "a9d36f2df8ec2ec3b1e0acd73370a2ce879e77cc06a9a9eab952838e10ce2641",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.7.12",
      "date": "2026-05-29T10:30:16.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "2773eb5ec75bc575954d31b41efa3d973a6681848077fb768218a8edb968d415",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.7.12",
      "date": "2026-05-29T10:30:13.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "b2726e3ca34b6937b1b19a84a3f44dc076521e42dc8f1bbae4ec1a35795a3b51",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.7.12",
      "date": "2026-05-29T10:30:21.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "2f5f74e6d991ef604287a949c08b07fa94d8705805fd2c732544a4142ae45f38",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.7.12",
      "date": "2026-05-29T11:40:37.000Z",
      "arch": "aarch64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "4297903ae175a7e128c6772672a0925b27fc3b649e2488c3ed1e553e82a2d6cf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.7.12",
      "date": "2026-05-29T10:32:37.000Z",
      "arch": "x86_64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "62500adf8a1b313c790ac630e7417cb058edc30337fcd56bd194a256f4a033cd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.7.12",
      "date": "2026-05-29T11:40:32.000Z",
      "arch": "aarch64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "07da19e26f72ac32d60ffb7152025cea00f19a4bbef868dc272d6d066b69992d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.7.12",
      "date": "2026-05-29T10:31:44.000Z",
      "arch": "x86_64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "fcdbf5c9c4da8bb4fec6a175cbb1e8954eeefb5593d329bb054a11ef18d975f2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.7.12",
      "date": "2026-05-29T10:30:14.000Z",
      "arch": "emscripten",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "4d5cf4d6e4aacefd91422804f17698ad1e31d992dd50081553a15b8005ed4fd9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.7.12",
      "date": "2026-05-29T10:29:38.000Z",
      "arch": "x86_64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "861d2872d48c809e43ad3033f1e3af7bd6866f29a85acad6aa016aa348ae869c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.7.12",
      "date": "2026-05-29T10:29:36.000Z",
      "arch": "x86_64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "a39feb337e772ad77534fa568bc51765ab61c76fda417381cb95c84d59b99beb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.7.12",
      "date": "2026-05-29T10:32:57.000Z",
      "arch": "x86_64",
      "commit": "5fd04bad2b069a8cb29fe49001d47eaf8c26b9e9",
      "fileid": "e2d4bb98e62c062ea8fb79e666e1df35da0f6f8d6e6392ddf188869f187562b0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cpanse/actions/runs/26631945895"
    }
  ]
}