{ "_id": "6ab0f5ad3d719c1f84085126", "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": "Bioconductor 3.23", "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": "2026-09-21 09:10:50 UTC", "User": "root" }, "Author": "Devon Kohler [aut, cre],\nMateusz Staniak [aut],\nCyril Galitzine [aut],\nMeena Choi [aut],\nOlga Vitek [aut]", "Maintainer": "Devon Kohler ", "_user": "bioc-release", "_type": "src", "_file": "MSstatsLOBD_1.20.0.tar.gz", "_fileid": "https://r2.ropensci.org/3b06e89ec7f6e61b719a847b6ea2b5fc8d107454f7a4ac2771387e7298fe4e8b", "_filesize": 1426861, "_sha256": "3b06e89ec7f6e61b719a847b6ea2b5fc8d107454f7a4ac2771387e7298fe4e8b", "_expires": "2026-12-30T09:15:23.000Z", "_created": "2026-09-21T09:10:50.000Z", "_published": "2026-09-21T09:15:25.258Z", "_bioccheck": { "error": 0, "warning": 1, "note": 13 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35581508323", "_status": "success", "_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": "Postdoctoral fellow at Northeastern University. Studying ML and statistics for computational biology", "uuid": 35807256 }, "_distro": "resolute", "_jobs": [ { "job": 106276273361, "time": 147, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "10630228979" }, { "job": 106276273498, "time": 178, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "10630238794" }, { "job": 106276273386, "time": 234, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "10630313834" }, { "job": 106276273420, "time": 91, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "10630388302" }, { "job": 106276273453, "time": 103, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "10630193933" }, { "job": 106275321740, "time": 196, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10630676266" }, { "job": 106276273468, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10630618011" }, { "job": 106276273604, "time": 86, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "10629894492" }, { "job": 106276273465, "time": 80, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "10629684882" }, { "job": 106276273464, "time": 88, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "10630742207" } ], "_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": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_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, "type": "organization", "name": "Bioconductor", "followers": 468, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 280, "source": "https://www.bioconductor.org/packages/stats/bioc/MSstatsLOBD" }, "_devurl": "https://github.com/vitek-lab/msstatslodq", "_searchresults": 6, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/MSstatsLOBD.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/vitek-lab/msstatslobd", "_realowner": "bioc", "_cranurl": false, "_exports": [ "linear_quantlim", "nonlinear_quantlim", "plot_quantlim" ], "_datasets": [ { "name": "raw_data", "title": "Example of dataset that contains spike in data for 43 distinct peptides.", "object": "raw_data", "class": [ "data.frame" ], "fields": [ "File.Name", "Sample.Name", "Replicate.Name", "Protein.Name", "Peptide.Sequence", "Peptide.Modified.Sequence", "Precursor.Charge", "Product.Charge", "Fragment.Ion", "Average.Measured.Retention.Time", "SampleGroup", "IS.Spike", "Concentration", "Replicate", "light.Area", "heavy.Area" ], "rows": 3870, "table": true, "tojson": true }, { "name": "spikeindata", "title": "Example of normalized datasets from raw_data,", "object": "spikeindata", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "INTENSITY", "CONCENTRATION", "NAME", "REPLICATE" ], "rows": 30, "table": true, "tojson": true } ], "_help": [ { "page": "linear_quantlim", "title": "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": "2026-09-21T09:13:35.000Z", "distro": "resolute", "commit": "f5e53eacaa5cfd9c55860e9b0b9543503f74c77c", "fileid": "https://r2.ropensci.org/248c54e42d4cdb54d3223220722ad040d0589944028264cd54accf43d9ed4491", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35581508323" }, { "r": "4.6.1", "os": "linux", "version": "1.20.0", "date": "2026-09-21T09:14:34.000Z", "distro": "resolute", "commit": "f5e53eacaa5cfd9c55860e9b0b9543503f74c77c", "fileid": "https://r2.ropensci.org/a40749e0b4dd61a3cea887524bfd48f7d9ac6dc2abdf4c6615df27e3439dfc65", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35581508323" }, { "r": "4.5.3", "os": "mac", "version": "1.20.0", "date": "2026-09-21T09:12:24.000Z", "commit": "f5e53eacaa5cfd9c55860e9b0b9543503f74c77c", "fileid": "https://r2.ropensci.org/011cd195a034d9667318c0079e12bc541093a095923558434ee1f5a8fc260aa6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35581508323" }, { "r": "4.6.1", "os": "mac", "version": "1.20.0", "date": "2026-09-21T09:12:35.000Z", "commit": "f5e53eacaa5cfd9c55860e9b0b9543503f74c77c", "fileid": "https://r2.ropensci.org/4b251d5adaf3b702b854ab97a2986b2a56048b5f0d6e1d741de4a39306f5dde0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35581508323" }, { "r": "4.6.0", "os": "wasm", "version": "1.20.0", "date": "2026-09-21T09:12:59.000Z", "commit": "f5e53eacaa5cfd9c55860e9b0b9543503f74c77c", "fileid": "https://r2.ropensci.org/2581f5b586e5da247a90d701d6c30bcb3363718f323470a6776f1ff3b8774d6b", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35581508323" }, { "r": "4.7.0", "os": "win", "version": "1.20.0", "date": "2026-09-21T09:11:59.000Z", "commit": "f5e53eacaa5cfd9c55860e9b0b9543503f74c77c", "fileid": "https://r2.ropensci.org/d77ede0cfac4ed922a3c53b5a2de746ca885bdbca35aa482631425c800aab04a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35581508323" }, { "r": "4.5.3", "os": "win", "version": "1.20.0", "date": "2026-09-21T09:12:00.000Z", "commit": "f5e53eacaa5cfd9c55860e9b0b9543503f74c77c", "fileid": "https://r2.ropensci.org/62485c3aa780fef7921ceea49424e05eebc672ef6fdfe07dbedcc798762b8677", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35581508323" }, { "r": "4.6.1", "os": "win", "version": "1.20.0", "date": "2026-09-21T09:12:02.000Z", "commit": "f5e53eacaa5cfd9c55860e9b0b9543503f74c77c", "fileid": "https://r2.ropensci.org/f3afe184c652b1bd5817cd8f547ea02a3ae3f3f9657fdee9d951ab400ee50418", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35581508323" } ] }