{
  "_id": "6a34f0c73efcd9bda43cfde1",
  "Package": "msmsEDA",
  "Type": "Package",
  "Title": "Exploratory Data Analysis of LC-MS/MS data by spectral counts",
  "Version": "1.50.0",
  "Date": "2014-01-19",
  "Author": "Josep Gregori, Alex Sanchez, and Josep Villanueva",
  "Maintainer": "Josep Gregori <josep.gregori@gmail.com>",
  "Description": "Exploratory data analysis to assess the quality of a set\nof LC-MS/MS experiments, and visualize de influence of the\ninvolved factors.",
  "License": "GPL-2",
  "Encoding": "latin1",
  "biocViews": "ImmunoOncology, Software, MassSpectrometry, Proteomics",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:37:58 UTC",
  "RemoteUrl": "https://github.com/bioc/msmsEDA",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "76eaebdc1072fb3c0a47606dbceeea5b75bd02d2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-19 07:26:04 UTC",
    "User": "root"
  },
  "MD5sum": "c1d19a7759c6c9bc7e1d799ccd938061",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "msmsEDA_1.50.0.tar.gz",
  "_fileid": "bb9cc1939286fb88be83ddef11f91186e6925b2e83b35a437a10c45aa4e6f532",
  "_filesize": 473169,
  "_sha256": "bb9cc1939286fb88be83ddef11f91186e6925b2e83b35a437a10c45aa4e6f532",
  "_created": "2026-06-19T07:26:04.000Z",
  "_published": "2026-06-19T07:33:27.237Z",
  "_jobs": [
    {
      "job": 82303890908,
      "time": 186,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7744083615"
    },
    {
      "job": 82303890914,
      "time": 278,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7744108666"
    },
    {
      "job": 82303890924,
      "time": 374,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7744135779"
    },
    {
      "job": 82303890961,
      "time": 167,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7744078231"
    },
    {
      "job": 82303890929,
      "time": 170,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7744079348"
    },
    {
      "job": 82303210298,
      "time": 299,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7744031746"
    },
    {
      "job": 82303890911,
      "time": 152,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7744074111"
    },
    {
      "job": 82303890952,
      "time": 250,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7744101920"
    },
    {
      "job": 82303890958,
      "time": 232,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7744096475"
    },
    {
      "job": 82303890932,
      "time": 211,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7744090148"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 2,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27811652740",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/msmsEDA",
  "_commit": {
    "id": "76eaebdc1072fb3c0a47606dbceeea5b75bd02d2",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379878
  },
  "_maintainer": {
    "name": "Josep Gregori",
    "email": "josep.gregori@gmail.com",
    "login": "josepgregori",
    "description": "",
    "uuid": 6534561
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.1",
      "role": "Depends"
    },
    {
      "package": "MSnbase",
      "role": "Depends"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.51.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.50.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "software",
    "massspectrometry",
    "proteomics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 2,
  "_searchresults": 4,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/msmsEDA.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "batch.neutralize",
    "count.stats",
    "counts.hc",
    "counts.heatmap",
    "counts.pca",
    "disp.estimates",
    "filter.flags",
    "gene.table",
    "norm.counts",
    "pp.msms.data",
    "spc.barplots",
    "spc.boxplots",
    "spc.densityplots",
    "spc.scatterplot"
  ],
  "_datasets": [
    {
      "name": "msms.dataset",
      "title": "LC-MS/MS dataset",
      "object": "msms.dataset",
      "file": "msms.dataset.rda",
      "class": [
        "MSnSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pnms",
      "title": "Accessions and gene symbols",
      "object": "pnms",
      "file": "pnms.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Accession",
        "Proteins"
      ],
      "rows": 1160,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "msmsEDA-package",
      "title": "Exploratory Data Analysis of label-free LC-MS/MS spectral counts",
      "topics": [
        "msmsEDA-package",
        "msmsEDA"
      ]
    },
    {
      "page": "batch.neutralize",
      "title": "Batch effects correction",
      "topics": [
        "batch.neutralize"
      ]
    },
    {
      "page": "count.stats",
      "title": "Summary of statistics of spectral counts by sample in the dataset",
      "topics": [
        "count.stats"
      ]
    },
    {
      "page": "counts.hc",
      "title": "Hierarchical clustering on an spectral counts matrix.",
      "topics": [
        "counts.hc"
      ]
    },
    {
      "page": "counts.heatmap",
      "title": "Heatmap of an spectral counts matrix.",
      "topics": [
        "counts.heatmap"
      ]
    },
    {
      "page": "counts.pca",
      "title": "Principal components analysis of an spectral counts matrix.",
      "topics": [
        "counts.pca"
      ]
    },
    {
      "page": "disp.estimates",
      "title": "Residual dispersion estimates",
      "topics": [
        "disp.estimates"
      ]
    },
    {
      "page": "filter.flags",
      "title": "Flag proteins with a minimum signal and/or sufficient dispersion.",
      "topics": [
        "filter.flags"
      ]
    },
    {
      "page": "gene.table",
      "title": "Gene symbols associated to protein accessions",
      "topics": [
        "gene.table"
      ]
    },
    {
      "page": "msms.dataset",
      "title": "LC-MS/MS dataset",
      "topics": [
        "msms.dataset"
      ]
    },
    {
      "page": "norm.counts",
      "title": "Spectral counts matrix normalization",
      "topics": [
        "norm.counts"
      ]
    },
    {
      "page": "pnms",
      "title": "Accessions and gene symbols",
      "topics": [
        "pnms"
      ]
    },
    {
      "page": "pp.msms.data",
      "title": "Spectral counts matrix pre-processing",
      "topics": [
        "pp.msms.data"
      ]
    },
    {
      "page": "spc.barplots",
      "title": "Set of SpC barplots by sample",
      "topics": [
        "spc.barplots"
      ]
    },
    {
      "page": "spc.boxplots",
      "title": "Set of SpC boxplots by sample",
      "topics": [
        "spc.boxplots"
      ]
    },
    {
      "page": "spc.densityplots",
      "title": "SpC density plots of a SpC matrix",
      "topics": [
        "spc.densityplots"
      ]
    },
    {
      "page": "spc.scatterplot",
      "title": "Scatterplot of SpC means comparing two conditions",
      "topics": [
        "spc.scatterplot"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "affy",
    "affyio",
    "AnnotationFilter",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "bitops",
    "bslib",
    "cachem",
    "caTools",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "DelayedArray",
    "digest",
    "dir.expiry",
    "doParallel",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "impute",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "magrittr",
    "MALDIquant",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "MetaboCoreUtils",
    "mime",
    "MsCoreUtils",
    "MSnbase",
    "MultiAssayExperiment",
    "mzID",
    "mzR",
    "ncdf4",
    "openssl",
    "otel",
    "pcaMethods",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "preprocessCore",
    "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",
    "xfun",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "msmsData-Vignette.Rnw",
      "filename": "msmsData-Vignette.pdf",
      "title": "msmsEDA: Batch effects detection in LC-MSMS experiments",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:31:28",
      "modified": "2014-01-19 10:57:55",
      "commits": 3
    }
  ],
  "_score": 4.380211241711606,
  "_indexed": false,
  "_nocasepkg": "msmseda",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/msmsEDA",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.50.0",
      "date": "2026-06-19T07:29:29.000Z",
      "distro": "noble",
      "commit": "76eaebdc1072fb3c0a47606dbceeea5b75bd02d2",
      "fileid": "e9fe80cb47b2f149c2da4171a6d392466c3cedf572e60240afbb75412f30332e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27811652740"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.50.0",
      "date": "2026-06-19T07:31:01.000Z",
      "distro": "noble",
      "commit": "76eaebdc1072fb3c0a47606dbceeea5b75bd02d2",
      "fileid": "210a587852808f5c486f996ca49107ed4f5f03a020d540ded157fa37367c7b16",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27811652740"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.50.0",
      "date": "2026-06-19T07:28:18.000Z",
      "commit": "76eaebdc1072fb3c0a47606dbceeea5b75bd02d2",
      "fileid": "5b731abdc8349e83e28d84106fe92584632bc68155ddfad417e06039aa55bf8a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27811652740"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.50.0",
      "date": "2026-06-19T07:28:19.000Z",
      "commit": "76eaebdc1072fb3c0a47606dbceeea5b75bd02d2",
      "fileid": "21bcc4d62ce41b826028c0734193e2256b0375dc9bfab176661d7ed354f4df4f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27811652740"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.50.0",
      "date": "2026-06-19T07:29:20.000Z",
      "commit": "76eaebdc1072fb3c0a47606dbceeea5b75bd02d2",
      "fileid": "90f58beeb5f54b174d1b3a1e25a03e6912904b219250a880f842a0a46c1b8aa6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27811652740"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.50.0",
      "date": "2026-06-19T07:28:20.000Z",
      "commit": "76eaebdc1072fb3c0a47606dbceeea5b75bd02d2",
      "fileid": "fa5d51c052347bcb87a24fdb660902f9ddd721053fd5b4aaa1b088a4d67dfbd8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27811652740"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.50.0",
      "date": "2026-06-19T07:28:26.000Z",
      "commit": "76eaebdc1072fb3c0a47606dbceeea5b75bd02d2",
      "fileid": "b023228e8667c1f1300626800f8d244541755ce38b1b68b9ac20443a7ab8cec0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27811652740"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.50.0",
      "date": "2026-06-19T07:28:05.000Z",
      "commit": "76eaebdc1072fb3c0a47606dbceeea5b75bd02d2",
      "fileid": "e480fa5548cca5c0d1112c7d2bd2f583ad06a11a9dc11afd63d4a72000b24de7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27811652740"
    }
  ]
}