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"title": "Example of output from proteinSummarizaiton function", "object": "quant.pd.msstats", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "raw.mine", "title": "Example of output from SpectroMine for TMT-6plex experiments.", "object": "raw.mine", "class": [ "data.frame" ], "fields": [ "R.MS3.Used", "R.BlockName", "R.QuantificationMethod", "R.FileName", "PG.Genes", "PG.Organisms", "PG.ProteinAccessions", "PG.ProteinDescriptions", "PG.ProteinNames", "PG.UniprotIds", "PG.Coverage", "PG.QValue", "PEP.IsProteinGroupSpecific", "PEP.IsProteotypic", "PEP.StrippedSequence", "PEP.QValue", "PEP.IsUsedForQuantification", "PP.Charge", "P.MoleculeID", "PSM.TMT6_126..Raw.", "PSM.TMT6_127..Raw.", "PSM.TMT6_128..Raw.", "PSM.TMT6_129..Raw.", "PSM.TMT6_130..Raw.", "PSM.TMT6_131..Raw.", "PSM.IsUsedForQuantification", "PSM.NrOfMatchedChannelIons", "PSM.Qvalue" ], "rows": 170, "table": true, "tojson": true }, { "name": "raw.om", "title": "Example of MSstatsTMT report from 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"topics": [ "proteinSummarization" ] }, { "page": "raw.mine", "title": "Example of output from SpectroMine for TMT-6plex experiments.", "topics": [ "raw.mine" ] }, { "page": "raw.om", "title": "Example of MSstatsTMT report from OpenMS for TMT-10plex experiments.", "topics": [ "raw.om" ] }, { "page": "raw.pd", "title": "Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments.", "topics": [ "raw.pd" ] }, { "page": "SpectroMinetoMSstatsTMTFormat", "title": "Import data from SpectroMine", "topics": [ "SpectroMinetoMSstatsTMTFormat" ] } ], "_readme": "https://github.com/bioc/MSstatsTMT/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "base64enc", "bitops", "boot", "bslib", "cachem", "caTools", "checkmate", "cli", "cpp11", "crosstalk", "curl", "data.table", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "ggrepel", "glue", "gplots", "gtable", "gtools", "highr", "htmltools", "htmlwidgets", "httr", "isoband", 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Staniak (mtst@mstaniak.pl), Sicheng Hao (hao.sic@husky.neu.edu), Olga Vitek(o.vitek@northeastern.edu)", "engine": "knitr::rmarkdown", "headings": [ "0. Load MSstatsTMT", "1. Converters for different peptide quantification tools", "PDtoMSstatsTMTFormat()", "Arguments", "Example", "MaxQtoMSstatsTMTFormat()", "SpectroMinetoMSstatsTMTFormat()", "OpenMStoMSstatsTMTFormat()", "PhilosophertoMSstatsTMTFormat()", "2. Protein summarization, normalization and visualization", "2.1. proteinSummarization()", "2.2 dataProcessPlotsTMT()", "3. groupComparisonTMT()" ], "created": "2017-12-13 04:07:58", "modified": "2022-02-18 18:39:31", "commits": 19 } ], "_score": 6.424064525417488, "_indexed": true, "_nocasepkg": "msstatstmt", "_universes": [ "bioc", "devonjkohler" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.21.0", "date": "2026-05-28T14:58:13.000Z", "distro": "noble", "commit": "1dff0916616921529e0512728a5085bc9f0cf62b", "fileid": "26900552e3e38087cb78d60ee5c0eeb37f6f80ecb5828605ad2976f1b29fd1e4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581988280" }, { "r": "4.6.0", "os": "linux", "version": "2.21.0", "date": "2026-05-28T14:59:48.000Z", "distro": "noble", "commit": "1dff0916616921529e0512728a5085bc9f0cf62b", "fileid": "5c1543d7ad51f270f441654e7b3af3bf3b7ee68d4ba58a0454357e6f29d16d78", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581988280" }, { "r": "4.5.3", "os": "mac", "version": "2.21.0", "date": "2026-05-28T15:51:15.000Z", "commit": "1dff0916616921529e0512728a5085bc9f0cf62b", "fileid": "516ce2b83724c3caf988b6353ff774bbb29100d6459e77a325e0be60e00ff954", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581988280" }, { "r": "4.6.0", "os": "mac", "version": "2.21.0", "date": "2026-05-28T15:54:18.000Z", "commit": "1dff0916616921529e0512728a5085bc9f0cf62b", "fileid": "af3d4c72e7b4fc3d653d3130baf25864722fa38e8f8a324c34b1ed44ae1c58f7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581988280" }, { "r": "4.6.0", "os": "wasm", "version": "2.21.0", "date": "2026-05-28T14:58:11.000Z", "commit": "1dff0916616921529e0512728a5085bc9f0cf62b", "fileid": "6a3d90d68f46eb79fea4911da7da177c7a7dca2e224718c861668d039e05b768", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581988280" }, { "r": "4.7.0", "os": "win", "version": "2.21.0", "date": "2026-05-28T14:56:57.000Z", "commit": "1dff0916616921529e0512728a5085bc9f0cf62b", "fileid": "a11005dd43077a52133ef9e5d303c7820075d2d31829dafa561f94ab3b453eb5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581988280" }, { "r": "4.5.3", "os": "win", "version": "2.21.0", "date": "2026-05-28T14:57:07.000Z", "commit": "1dff0916616921529e0512728a5085bc9f0cf62b", "fileid": "99599fbdb4e11901271c02558037f6b372de642dee14f781a6f992224163c3a7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581988280" }, { "r": "4.6.0", "os": "win", "version": "2.21.0", "date": "2026-05-28T14:56:53.000Z", "commit": "1dff0916616921529e0512728a5085bc9f0cf62b", "fileid": "8cfa9067fd0d4205dfd90a4551ae997e4064e80368b018718d4f6e75f2d2be36", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581988280" } ] }