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Requires input from dataSummarizationLiP function. Can optionally calculate differential analysis using proteolytic resistance. In order for this function to work, Conditions and run numbers must match between the LiP and TrP data.", "topics": [ "calculateProteolyticResistance" ] }, { "page": "calculateTrypticity", "title": "Calculates level of trypticity for a list of LiP Peptides.", "topics": [ "calculateTrypticity" ] }, { "page": "correlationPlotLiP", "title": "Plot run correlation for provided LiP and TrP experiment.", "topics": [ "correlationPlotLiP" ] }, { "page": "dataProcessPlotsLiP", "title": "Visualization for explanatory data analysis", "topics": [ "dataProcessPlotsLiP" ] }, { "page": "dataSummarizationLiP", "title": "Summarizes LiP and TrP datasets seperately using methods from MSstats.", "topics": [ "dataSummarizationLiP" ] }, { "page": "DIANNtoMSstatsLiPFormat", "title": "Converts raw LiP MS data from DIA-NN into the format needed for MSstatsLiP.", "topics": [ "DIANNtoMSstatsLiPFormat" ] }, { "page": "groupComparisonLiP", "title": "Model LiP and TrP data and make adjustments if needed Returns list of three modeled datasets", "topics": [ "groupComparisonLiP" ] }, { "page": "groupComparisonPlotsLiP", "title": "Visualization for model-based analysis and summarization", "topics": [ "groupComparisonPlotsLiP" ] }, { "page": "LiPRawData", "title": "LiPRawData", "topics": [ "LiPRawData" ] }, { "page": "locateMod", "title": "Locate modified sites with a peptide", "topics": [ "locateMod" ] }, { "page": "locatePTM", "title": "Annotate modified sites with associated peptides", "topics": [ "locatePTM" ] }, { "page": "MSstatsLiP_data", "title": "MSstatsLiP_data", "topics": [ "MSstatsLiP_data" ] }, { "page": "MSstatsLiP_model", "title": "MSstatsLiP_model", "topics": [ "MSstatsLiP_model" ] }, { "page": "MSstatsLiP_Summarized", "title": "MSstatsLiP_Summarized", "topics": [ "MSstatsLiP_Summarized" ] }, { "page": "PCAPlotLiP", "title": "Visualize PCA analysis for LiP and TrP datasets.", "topics": [ "PCAPlotLiP" ] }, { "page": "raw_lip", "title": "raw_lip", "topics": [ "raw_lip" ] }, { "page": "raw_prot", "title": "raw_prot", "topics": [ "raw_prot" ] }, { "page": "ResistanceBarcodePlotLiP", "title": "Proteolytic Resistance Barcode plot. 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Installation", "2. Data preprocessing", "2.1 Load datasets", "2.2 Select only fully tryptic (FT) peptides in both LiP and TrP dataset", "2.3 Correct nomenclature", "Step 1:", "Step 2:", "2.4 Data Summarization", "3. Modelling", "4. Calculate proteolytic resistance ratios", "5. Proteolytic resistance differential analysis", "6. Save outputs", "7. Plot aSynuclein proteolytic resistance DA result as barcode" ], "created": "2022-04-18 20:34:56", "modified": "2022-09-27 18:11:13", "commits": 4 }, { "source": "MSstatsLiP_Workflow.Rmd", "filename": "MSstatsLiP_Workflow.html", "title": "MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP package", "author": "Devon Kohler (kohler.d@northeastern.edu)", "engine": "knitr::rmarkdown", "headings": [ "MSstatsLiP Workflow Vignette", "Installation", "Workflow", "1. Preprocessing", "1.1 Raw Data Format", "1.2 Converter", "2. Summarization", "2.1 Summarization Function", "2.2 Tryptic barplot", "2.3 Run Correlation Plot", "2.4 Coefficient of Variation", "2.5 QCPlot", "2.6 Profile Plot", "2.7 PCA Plot", "2.8 Calculate Trypticity", "3. Modeling", "3.1 Function", "3.2 Volcano Plot", "3.3 Heatmap", "3.4 Barcode", "3.5 Calculate proteolytic resistance ratios" ], "created": "2021-03-11 20:46:05", "modified": "2022-09-27 18:11:13", "commits": 17 } ], "_score": 6.225309281725863, "_indexed": true, "_nocasepkg": "msstatslip", "_universes": [ "bioc", "tonywu1999", "vitek-lab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-05-28T14:43:47.000Z", "distro": "noble", "arch": "aarch64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "be5ac1d29f3474f9f7ff1c7b1b84895030b7560c5a36316e2827f8280717ff1f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-05-28T14:44:13.000Z", "distro": "noble", "arch": "x86_64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "2aac4b688aa58fa510fe3f5aa869a80cb4cacdeb12b0de9fbb48ddbca3868c26", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.6.0", "os": "linux", "version": "1.19.0", "date": "2026-05-28T14:43:15.000Z", "distro": "noble", "arch": "aarch64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "03eb3e8e6bb2fa30a8bf0516c2bdd04e2eb76e2adbfba1a4349b4e1aba463421", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.6.0", "os": "linux", "version": "1.19.0", "date": "2026-05-28T14:44:28.000Z", "distro": "noble", "arch": "x86_64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "01aecc6cb5d972591bfd68613c71994c5a80bf2bf752dc6715ae0421b160972a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-05-28T14:53:08.000Z", "arch": "aarch64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "bf276a12ff5c6d8f0d8f2a7961300c660935a1884507e85a49f7aa390e24fc96", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-05-28T14:53:44.000Z", "arch": "x86_64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "1afb5185aa760310c9119733992aa278cadff0a5218a5f7a3528d9f8d01ab0b3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.6.0", "os": "mac", "version": "1.19.0", "date": "2026-05-28T14:55:48.000Z", "arch": "aarch64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "d6486f099e98fcf3e32c7f04bb83234b311bb7126e4cc505077a68ddc3d57636", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.6.0", "os": "mac", "version": "1.19.0", "date": "2026-05-28T14:51:54.000Z", "arch": "x86_64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "258cd2fe10a82faecfbc73673511308358e55fb65f7ce32af410c49a8d4908d5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-05-28T14:44:18.000Z", "arch": "emscripten", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "7d90fb3683803dc094ad30a92f63074f346621d5cda948ac93165ec245109b7d", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-05-28T14:42:05.000Z", "arch": "x86_64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "dfe3c9a31cb131106b29efb57ecec778ba78cd61a79ba373374b9ffd223c01f0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.5.3", "os": "win", "version": "1.19.0", "date": "2026-05-28T14:42:14.000Z", "arch": "x86_64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "b933d035c9a34568f28461d81df383438904a5f868f63f9e477d70a75053f7e6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" }, { "r": "4.6.0", "os": "win", "version": "1.19.0", "date": "2026-05-28T14:42:06.000Z", "arch": "x86_64", "commit": "28c13fd171296fc12b2b396b1ab58a2d530218b2", "fileid": "c5cdb359146dcb4b82b68e445e2d2cb2b61758c5c8d6dd0b37dbd135158789c5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581382227" } ] }