{ "_id": "6a195070acfb0bcc41ddf5dc", "Type": "Package", "Package": "MSstatsLOBD", "Title": "Assay characterization: estimation of limit of blanc(LoB) and\nlimit of detection(LOD)", "Version": "1.20.0", "Date": "2021-04-12", "Description": "The MSstatsLOBD package allows calculation and\nvisualization of limit of blac (LOB) and limit of detection\n(LOD). We define the LOB as the highest apparent concentration\nof a peptide expected when replicates of a blank sample\ncontaining no peptides are measured. The LOD is defined as the\nmeasured concentration value for which the probability of\nfalsely claiming the absence of a peptide in the sample is\n0.05, given a probability 0.05 of falsely claiming its\npresence. These functionalities were previously a part of the\nMSstats package. The methodology is described in Galitzine\n(2018) .", "Authors@R": "c(person(\"Devon\", \"Kohler\", email = \"kohler.d@northeastern.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Mateusz\", \"Staniak\", email = \"mtst@mstaniak.pl\", role = c(\"aut\")),\nperson(\"Cyril\", \"Galitzine\", email = \"cyrildgg@gmail.com\", role = \"aut\"),\nperson(\"Meena\", \"Choi\", email = \"mnchoi67@gmail.com\", role=\"aut\"),\nperson(\"Olga\", \"Vitek\", email = \"o.vitek@northeastern.edu\", role = \"aut\"))", "License": "Artistic-2.0", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, MassSpectrometry, Proteomics, Software,\nDifferentialExpression, OneChannel, TwoChannel, Normalization,\nQualityControl", "BugReports": "https://github.com/Vitek-Lab/MSstatsLODQ/issues", "Encoding": "UTF-8", "LazyData": "TRUE", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.1", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:56:14 UTC", "RemoteUrl": "https://github.com/bioc/MSstatsLOBD", "RemoteRef": "RELEASE_3_23", "RemoteSha": "f5e53eacaa5cfd9c55860e9b0b9543503f74c77c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:31:00 UTC", "User": "root" }, "Author": "Devon Kohler [aut, cre],\nMateusz Staniak [aut],\nCyril Galitzine [aut],\nMeena Choi [aut],\nOlga Vitek [aut]", "Maintainer": "Devon Kohler ", "MD5sum": "79fc8102fe02eddfc08a6f371903c915", "_user": "bioc-release", "_type": "src", "_file": "MSstatsLOBD_1.20.0.tar.gz", "_fileid": "19dbc30984c3ea943c691ea411704320fc40b850c98fc929dcab17684f239b29", "_filesize": 1433577, "_sha256": "19dbc30984c3ea943c691ea411704320fc40b850c98fc929dcab17684f239b29", "_created": "2026-05-29T07:31:00.000Z", "_published": "2026-05-29T08:38:08.446Z", "_jobs": [ { "job": 78457588743, "time": 143, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7285485706" }, { "job": 78457588698, "time": 152, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7285488412" }, { "job": 78457588699, "time": 153, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7285488703" }, { "job": 78457588692, "time": 83, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7286590545" }, { "job": 78457588684, "time": 101, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7286591514" }, { "job": 78457184204, "time": 171, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285443737" }, { "job": 78457588671, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285476473" }, { "job": 78457588721, "time": 94, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7285471626" }, { "job": 78457588723, "time": 91, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7285471071" }, { "job": 78457588736, "time": 91, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7285470958" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624272384", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MSstatsLOBD", "_commit": { "id": "f5e53eacaa5cfd9c55860e9b0b9543503f74c77c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380974 }, "_maintainer": { "name": "Devon Kohler", "email": "kohler.d@northeastern.edu", "login": "devonjkohler", "linkedin": "in/devon-kohler-5a52a032", "twitter": "@devonjkohler", "description": "PhD student at Northeastern University. 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"Calculation of the LOB and LOD with a linear fit", "topics": [ "linear_quantlim" ] }, { "page": "nonlinear_quantlim", "title": "Calculation of the LOB and LOD with a nonlinear fit", "topics": [ "nonlinear_quantlim" ] }, { "page": "plot_quantlim", "title": "Plot results of nonlinear_quantlim() and linear_quantlim()", "topics": [ "plot_quantlim" ] }, { "page": "raw_data", "title": "Example of dataset that contains spike in data for 43 distinct peptides.", "topics": [ "raw_data" ] }, { "page": "spikeindata", "title": "Example of normalized datasets from raw_data,", "topics": [ "spikeindata" ] } ], "_readme": "https://github.com/bioc/MSstatsLOBD/raw/RELEASE_3_23/README.md", "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "minpack.lm", "R6", "RColorBrewer", "Rcpp", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "MSstatsLOBD_workflow.Rmd", "filename": "MSstatsLOBD_workflow.html", "title": "LOB/LOD Estimation Workflow", "author": "Cyril Galitzine", "engine": "knitr::rmarkdown", "headings": [ "Installation", "1 Example dataset", "1 Introduction", "2 Loading and Normalization of the data", "2.1 Load the raw data file and check its content.", "2.2 Normalize Dataset", "3 LOB/LOD definitions", "3.1 Assay characterization procedure", "3.2 LOB/LOD definitions", "4 Estimation of the LOB/LOD for dataset", "4.1 LOB/LOD estimation for a non-linear peptide", "4.2 LOB/LOD estimation for a linear peptide", "4.3 LOB/LOD linear estimation for a non-linear peptide", "4.4 LOB/LOD linear estimation for a linear peptide", "REFERENCES" ], "created": "2021-04-23 00:03:47", "modified": "2021-04-23 13:41:11", "commits": 2 } ], "_score": 4.301029995663981, "_indexed": false, "_nocasepkg": "msstatslobd", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/MSstatsLOBD", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-05-29T07:33:20.000Z", 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