{
  "_id": "6ad34f94de48616761a36bb5",
  "Package": "msmsTests",
  "Type": "Package",
  "Title": "LC-MS/MS Differential Expression Tests",
  "Version": "1.51.0",
  "Date": "2013-10-02",
  "Author": "Josep Gregori, Alex Sanchez, and Josep Villanueva",
  "Maintainer": "Josep Gregori i Font <josep.gregori@gmail.com>",
  "Description": "Statistical tests for label-free LC-MS/MS data by spectral\ncounts, to discover differentially expressed proteins between\ntwo biological conditions. Three tests are available: Poisson\nGLM regression, quasi-likelihood GLM regression, and the\nnegative binomial of the edgeR package.The three models admit\nblocking factors to control for nuissance variables.To assure a\ngood level of reproducibility a post-test filter is available,\nwhere we may set the minimum effect size considered biologicaly\nrelevant, and the minimum expression of the most abundant\ncondition.",
  "License": "GPL-2",
  "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.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:00 UTC",
  "RemoteUrl": "https://github.com/bioc/msmsTests",
  "RemoteRef": "HEAD",
  "RemoteSha": "36efb3a9419a448d69c5110a2990472703b43e6d",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-17 10:11:20 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "msmsTests_1.51.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/2590f81fc056ce380fe79851e15ec003572b361d9e1089ea57cbb9fead20eb7b",
  "_filesize": 436465,
  "_sha256": "2590f81fc056ce380fe79851e15ec003572b361d9e1089ea57cbb9fead20eb7b",
  "_expires": "2027-01-25T10:18:21.000Z",
  "_created": "2026-10-17T10:11:20.000Z",
  "_published": "2026-10-17T10:36:04.777Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39023659212",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 13
  },
  "_upstream": "https://github.com/bioc/msmsTests",
  "_commit": {
    "id": "36efb3a9419a448d69c5110a2990472703b43e6d",
    "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": 1777379880
  },
  "_maintainer": {
    "name": "Josep Gregori i Font",
    "email": "josep.gregori@gmail.com",
    "login": "josepgregori",
    "description": "",
    "uuid": 6534561
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 117375047688,
      "time": 168,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12098676161"
    },
    {
      "job": 117375048580,
      "time": 352,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12098375468"
    },
    {
      "job": 117375048400,
      "time": 332,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12097589273"
    },
    {
      "job": 117375048858,
      "time": 233,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12098345369"
    },
    {
      "job": 117375048631,
      "time": 272,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12098300543"
    },
    {
      "job": 117375073407,
      "time": 299,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12097871835"
    },
    {
      "job": 117375048488,
      "time": 153,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12096874495"
    },
    {
      "job": 117375048218,
      "time": 164,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12097623759"
    },
    {
      "job": 117375048459,
      "time": 238,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12098105630"
    },
    {
      "job": 117375048610,
      "time": 225,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12097464926"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.1",
      "role": "Depends"
    },
    {
      "package": "MSnbase",
      "role": "Depends"
    },
    {
      "package": "msmsEDA",
      "role": "Depends"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "qvalue",
      "role": "Imports"
    },
    {
      "package": "xtable",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.51.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.50.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "immunooncology",
    "software",
    "massspectrometry",
    "proteomics"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 477,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 713,
    "source": "https://www.bioconductor.org/packages/stats/bioc/msmsTests"
  },
  "_mentions": 4,
  "_searchresults": 19,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/msmsTests.html"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "msms.edgeR",
    "msms.glm.pois",
    "msms.glm.qlll",
    "pval.by.fc",
    "res.volcanoplot",
    "test.results"
  ],
  "_datasets": [
    {
      "name": "msms.spk",
      "title": "Yeast lisate samples spiked with human proteins",
      "object": "msms.spk",
      "file": "msms.spk.rda",
      "class": [
        "MSnSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "msmsTests-package",
      "title": "LC-MS/MS Differential Expression Tests",
      "topics": [
        "msmsTests-package",
        "msmsTests"
      ]
    },
    {
      "page": "msms.edgeR",
      "title": "Spectral counts differential expression by edgeR",
      "topics": [
        "msms.edgeR"
      ]
    },
    {
      "page": "msms.glm.pois",
      "title": "Spectral counts differential expression by Poisson GLM",
      "topics": [
        "msms.glm.pois"
      ]
    },
    {
      "page": "msms.glm.qlll",
      "title": "Spectral counts differential expression by quasi-likelihood GLM",
      "topics": [
        "msms.glm.qlll"
      ]
    },
    {
      "page": "msms.spk",
      "title": "Yeast lisate samples spiked with human proteins",
      "topics": [
        "msms.spk"
      ]
    },
    {
      "page": "pval.by.fc",
      "title": "Table of cumulative frequencies of p-values by log fold change bins",
      "topics": [
        "pval.by.fc"
      ]
    },
    {
      "page": "res.volcanoplot",
      "title": "Volcanoplot",
      "topics": [
        "res.volcanoplot"
      ]
    },
    {
      "page": "test.results",
      "title": "Multitest p-value adjustment and post-test filter",
      "topics": [
        "test.results"
      ]
    }
  ],
  "_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",
    "edgeR",
    "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",
    "locfit",
    "magrittr",
    "MALDIquant",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "MetaboCoreUtils",
    "mime",
    "MsCoreUtils",
    "msmsEDA",
    "MSnbase",
    "MultiAssayExperiment",
    "mzID",
    "mzR",
    "ncdf4",
    "openssl",
    "otel",
    "pcaMethods",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "preprocessCore",
    "promises",
    "ProtGenerics",
    "PSMatch",
    "PTMods",
    "purrr",
    "QFeatures",
    "qvalue",
    "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": "msmsTests-Vignette2.Rnw",
      "filename": "msmsTests-Vignette2.pdf",
      "title": "msmsTests: controlling batch effects by blocking",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:31:38",
      "modified": "2013-11-01 20:31:38",
      "commits": 1
    },
    {
      "source": "msmsTests-Vignette.Rnw",
      "filename": "msmsTests-Vignette.pdf",
      "title": "msmsTests: post test filters to improve reproducibility",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:31:38",
      "modified": "2013-11-01 20:31:38",
      "commits": 1
    }
  ],
  "_score": 4.9599948383284165,
  "_indexed": true,
  "_nocasepkg": "msmstests",
  "_universes": [
    "bioc",
    "josepgregori"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.51.0",
      "date": "2026-10-17T10:15:30.000Z",
      "distro": "resolute",
      "commit": "36efb3a9419a448d69c5110a2990472703b43e6d",
      "fileid": "https://r2.ropensci.org/81114d22afea9f0e4e13bacca1a9a846dbecd081e4067850369cdf56b94c3196",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023659212"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.51.0",
      "date": "2026-10-17T10:15:14.000Z",
      "distro": "resolute",
      "commit": "36efb3a9419a448d69c5110a2990472703b43e6d",
      "fileid": "https://r2.ropensci.org/ee754fb00ca1d19a74faf8bfcd1e4dc8d7d9e11789ba486f81769fb0af7b1ee4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023659212"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.51.0",
      "date": "2026-10-17T10:14:00.000Z",
      "commit": "36efb3a9419a448d69c5110a2990472703b43e6d",
      "fileid": "https://r2.ropensci.org/835da2ceeca1bfa8364ce45ccc0f493723df663a3ba3f0007e4ff2ba3bef6017",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023659212"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.51.0",
      "date": "2026-10-17T10:14:03.000Z",
      "commit": "36efb3a9419a448d69c5110a2990472703b43e6d",
      "fileid": "https://r2.ropensci.org/d5df9e5ae498810087d656e756bafcf0a5f59e7d42de1c2d465cb6c59075afb6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023659212"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.51.0",
      "date": "2026-10-17T10:14:35.000Z",
      "commit": "36efb3a9419a448d69c5110a2990472703b43e6d",
      "fileid": "https://r2.ropensci.org/84454f9a85146869f20021429e2bf141f383f5996961c1190920d8008fa696be",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023659212"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-10-17T10:13:07.000Z",
      "commit": "36efb3a9419a448d69c5110a2990472703b43e6d",
      "fileid": "https://r2.ropensci.org/2d01faeed808e75224e1d099cd375beb9c41dde6a7ee1181e8c9482b4eb78cbf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023659212"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-10-17T10:13:24.000Z",
      "commit": "36efb3a9419a448d69c5110a2990472703b43e6d",
      "fileid": "https://r2.ropensci.org/bba67dc39773f1147958375ecc3accb035aad4b36b338b39efaa83352cf6de43",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023659212"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.51.0",
      "date": "2026-10-17T10:13:25.000Z",
      "commit": "36efb3a9419a448d69c5110a2990472703b43e6d",
      "fileid": "https://r2.ropensci.org/1173886e67bbdbe15a361b8962fecaab4301aa905bb8185f283563093ad73577",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39023659212"
    }
  ]
}