{ "_id": "6a103cb5acfb0bcc41c9c044", "Type": "Package", "Package": "MSstatsLOBD", "Title": "Assay characterization: estimation of limit of blanc(LoB) and\nlimit of detection(LOD)", "Version": "1.21.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:56:14 UTC", "RemoteUrl": "https://github.com/bioc/MSstatsLOBD", "RemoteRef": "HEAD", "RemoteSha": "7c554880e0a8630e754ffa280ec71a69be20c1f5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 10:07:26 UTC", "User": "root" }, "Author": "Devon Kohler [aut, cre],\nMateusz Staniak [aut],\nCyril Galitzine [aut],\nMeena Choi [aut],\nOlga Vitek [aut]", "Maintainer": "Devon Kohler ", "MD5sum": "d46cb255c95df2a67afb0fcb35093d13", "_user": "bioc", "_type": "src", "_file": "MSstatsLOBD_1.21.0.tar.gz", "_fileid": "eadb2af25b2f877bf70d5389b2402d254c30655f244edbed2b633fdb6b005fb6", "_filesize": 1454584, "_sha256": "eadb2af25b2f877bf70d5389b2402d254c30655f244edbed2b633fdb6b005fb6", "_created": "2026-05-11T10:07:26.000Z", "_published": "2026-05-22T11:23:33.489Z", "_jobs": [ { "job": 77369755644, "time": 145, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "6915721370" }, { "job": 77369755612, "time": 197, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6915740611" 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"error": 0, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25663561686", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MSstatsLOBD", "_commit": { "id": "7c554880e0a8630e754ffa280ec71a69be20c1f5", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following 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", "uuid": 35807256 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "minpack.lm", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "tinytest", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "massspectrometry", "proteomics", "software", "differentialexpression", "onechannel", "twochannel", "normalization", "qualitycontrol", "mass-spectrometry" ], "_stars": 0, "_contributors": [ { "user": "mstaniak", "count": 29, "uuid": 20418265 }, { "user": "devonjkohler", "count": 16, "uuid": 35807256 }, { "user": "meenachoi", "count": 7, "uuid": 4159931 } ], "_userbio": { "uuid": 2286807, 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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/HEAD/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": true, "_nocasepkg": "msstatslobd", "_universes": [ "bioc", "devonjkohler", "vitek-lab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-05-11T10:10:44.000Z", "distro": "noble", "commit": "7c554880e0a8630e754ffa280ec71a69be20c1f5", "fileid": "146246c01ebbad43620af0c00c294127e3ec39fa3a69e349c9d22bd62aac2a3f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25663561686" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-05-11T10:10:27.000Z", "distro": "noble", "commit": "7c554880e0a8630e754ffa280ec71a69be20c1f5", "fileid": 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