{ "_id": "6a1be7251d7bb097a0a1ac3e", "Package": "CalibraCurve", "Title": "Calibration curves for targeted proteomics, lipidomics and\nmetabolomics data", "Version": "1.3.0", "Authors@R": "c(\nperson(\"Karin\", \"Schork\", , \"karin.schork@rub.de\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3756-4347\")),\nperson(\"Robin\", \"Grugel\", , \"robin.grugel@rub.de\", role = c(\"aut\")),\nperson(\"Michael\", \"Kohl\", , , role = c(\"aut\")),\nperson(\"Markus\", \"Stepath\", , , role = c(\"aut\")),\nperson(\"Martin\", \"Eisenacher\", , \"martin.eisenacher@rub.de\", role = c(\"aut\", \"fnd\")))", "Description": "CalibraCurve is a computational tool designed to generate\ncalibration curves for targeted mass spectrometry-based\nquantitative data. It is applicable to various omics\ndisciplines, including proteomics, lipidomics, and\nmetabolomics. The package also offers functionalities for data\nand calibration curve visualization and concentration\nprediction from new datasets based on the established curves.", "License": "BSD 3-clause License + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "biocViews": "Proteomics, Lipidomics, Metabolomics, Regression,\nMassSpectrometry, Visualization", "URL": "https://github.com/mpc-bioinformatics/CalibraCurve", "BugReports": "https://github.com/mpc-bioinformatics/CalibraCurve/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:05:42 UTC", "RemoteUrl": "https://github.com/bioc/CalibraCurve", "RemoteRef": "HEAD", "RemoteSha": "7140fc647bf03fcfe2ace98eb66a1d59181d380a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 06:41:27 UTC", "User": "root" }, "Author": "Karin Schork [aut, cre] (ORCID:\n),\nRobin Grugel [aut],\nMichael Kohl [aut],\nMarkus Stepath [aut],\nMartin Eisenacher [aut, fnd]", "Maintainer": "Karin Schork ", "MD5sum": "67965f03e76535039995d9848171e133", "_user": "bioc", "_type": "src", "_file": "CalibraCurve_1.3.0.tar.gz", "_fileid": "9436ac38edd7111773c131aadee60799048ba8a9fd6560250608dc5ce99b3334", "_filesize": 1632813, "_sha256": "9436ac38edd7111773c131aadee60799048ba8a9fd6560250608dc5ce99b3334", "_created": "2026-05-31T06:41:27.000Z", "_published": "2026-05-31T07:45:40.990Z", "_jobs": [ { "job": 78706277663, "time": 189, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7314531592" }, { "job": 78706277675, "time": 312, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7314543780" }, { "job": 78706277681, "time": 257, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7314538449" }, { "job": 78706277697, "time": 210, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7314933787" }, { "job": 78706277685, "time": 181, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7314930795" }, { "job": 78706070965, "time": 244, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7314512885" }, { "job": 78706277651, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7314525485" }, { "job": 78706277693, "time": 224, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7314535072" }, { "job": 78706277701, "time": 245, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7314537764" }, { "job": 78706277721, "time": 200, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7314532553" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 2 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26705548278", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CalibraCurve", "_commit": { "id": "7140fc647bf03fcfe2ace98eb66a1d59181d380a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381542 }, "_maintainer": { "name": "Karin Schork", "email": "karin.schork@rub.de", "login": "karinschork", "description": "Statistician in the proteomics field", "uuid": 6604866, "orcid": "0000-0003-3756-4347" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "checkmate", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "openxlsx", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "msqc1", "role": "Suggests" }, { "package": "RefManageR", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "sessioninfo", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "vdiffr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-23", "n": 2 }, { "week": "2025-25", "n": 4 }, { "week": "2025-26", "n": 7 }, { "week": "2025-28", "n": 2 }, { "week": "2025-29", "n": 3 }, { "week": "2025-30", "n": 7 }, { "week": "2025-31", "n": 2 }, { "week": "2025-40", "n": 8 }, { "week": "2025-41", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2025-46", "n": 8 }, { "week": "2025-48", "n": 1 }, { "week": "2026-10", "n": 6 }, { "week": "2026-11", "n": 2 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.3.0", "bioc": "3.24" }, { "branch": "release", "version": "1.2.0", "bioc": "3.23" } ], "_topics": [ "proteomics", "lipidomics", "metabolomics", "regression", "massspectrometry", "visualization", "assays", "calibration", "dynamic-linear-ranges", "quantification-limits", "targeted-proteomics" ], "_stars": 5, "_contributors": [ { "user": "karinschork", "count": 126, "uuid": 6604866 }, { "user": "mstepath", "count": 4, "uuid": 70260274 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "robingrugel", "count": 1, "uuid": 26432538 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 217, "source": "https://www.bioconductor.org/packages/stats/bioc/CalibraCurve" }, "_devurl": "https://github.com/mpc-bioinformatics/calibracurve", "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/CalibraCurve.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/mpc-bioinformatics/calibracurve", "_realowner": "bioc", "_cranurl": false, "_exports": [ "assemble_results", "calc_single_curve", "calcRF", "calculate_FLR", "calculate_PLR", "CalibraCurve", "cleanData", "plotCalibraCurve", "plotResponseFactors", "predictConcentration", "readDataSE", "readDataTable", "readMultipleTables" ], "_help": [ { "page": "dot-calcContPrelimRanges", "title": "PLR: Calculate key features for the existing continuous preliminary ranges", "topics": [ ".calcContPrelimRanges" ] }, { "page": "dot-calcCV", "title": "PLR: calculate CV for one concentration level", "topics": [ ".calcCV" ] }, { "page": "dot-calcLinearModel", "title": "FLR: calculate weighted or unweighted linear model", "topics": [ ".calcLinearModel" ] }, { "page": "dot-calcPerBias", "title": "FLR: calculate percent bias for a specific concentration level", "topics": [ ".calcPerBias" ] }, { "page": "dot-calcPerBiasAvgSDCV", "title": "FLR: calculate average, SD and CV percent bias for each concentration level", "topics": [ ".calcPerBiasAvgSDCV" ] }, { "page": "dot-calcPerBiasLevels", "title": "FLR: calculate list of percent bias values for all concentration levels", "topics": [ ".calcPerBiasLevels" ] }, { "page": "dot-calcResponseFactors", "title": "Calculate Response factors", "topics": [ ".calcResponseFactors" ] }, { "page": "dot-calcWeights", "title": "FLR: calculate weights for linear model for a specific concentration level", "topics": [ ".calcWeights" ] }, { "page": "dot-checkFinalRange", "title": "FLR: checks if final linear range has been reached (compare average percent bias with threshold)", "topics": [ ".checkFinalRange" ] }, { "page": "dot-checkNumberReplicates", "title": "Data preprocessing: Helper function to check for sufficient number of replicates for a specific concentration level", "topics": [ ".checkNumberReplicates" ] }, { "page": "dot-filterConcentrationLevel", "title": "Data preprocessing: Helper function to select all rows from a specific concentration level", "topics": [ ".filterConcentrationLevel" ] }, { "page": "dot-prepareAnnotationData", "title": "Prepare annotation data", "topics": [ ".prepareAnnotationData" ] }, { "page": "dot-prepareCalibData", "title": "Prepare calibration data", "topics": [ ".prepareCalibData" ] }, { "page": "dot-prepareCurveData", "title": "Prepare curve data", "topics": [ ".prepareCurveData" ] }, { "page": "dot-saveCCResult", "title": "Save results of CalibraCurve", "topics": [ ".saveCCResult" ] }, { "page": "dot-saveTablesAndPlots", "title": "Save result tables and plots", "topics": [ ".saveTablesAndPlots" ] }, { "page": "dot-selctConcLevel", "title": "FLR: selects the highest or lowest concentration level for removal", "topics": [ ".selctConcLevel" ] }, { "page": "assemble_results", "title": "Assemble result tables", "topics": [ "assemble_results" ] }, { "page": "calc_single_curve", "title": "Calculate all necessary steps for a single calibration curve", "topics": [ "calc_single_curve" ] }, { "page": "calcRF", "title": "Calculate Response factors", "topics": [ "calcRF" ] }, { "page": "calculate_FLR", "title": "Calculate the final linear range", "topics": [ "calculate_FLR" ] }, { "page": "calculate_PLR", "title": "Calculate preliminary linear range (PLR)", "topics": [ "calculate_PLR" ] }, { "page": "CalibraCurve", "title": "CalibraCurve", "topics": [ "CalibraCurve" ] }, { "page": "cleanData", "title": "Clean data (remove 0s and NAs, remove concentration levels with insufficient number of replicates)", "topics": [ "cleanData" ] }, { "page": "plotCalibraCurve", "title": "Plot the calibration curve", "topics": [ "plotCalibraCurve" ] }, { "page": "plotResponseFactors", "title": "Plot response factors", "topics": [ "plotResponseFactors" ] }, { "page": "predictConcentration", "title": "Predict concentrations from intensity values based on a given calibration curve", "topics": [ "predictConcentration" ] }, { "page": "readDataSE", "title": "Read data stored as an SummarizedExperiment object (directly or stored in an .rds file). Extracts the two relevant columns (concentration and measurement) and orders the data by increasing concentration level.", "topics": [ "readDataSE" ] }, { "page": "readDataTable", "title": "Read data in different table input formats (xlsx, csv or txt). Extracts the two relevant columns (concentration and measurement) and orders the data by increasing concentration.", "topics": [ "readDataTable" ] }, { "page": "readMultipleTables", "title": "Read folder of files in different table input formats (xlsx, csv or txt).", "topics": [ "readMultipleTables" ] } ], "_readme": "https://github.com/bioc/CalibraCurve/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "Biobase", "BiocGenerics", "checkmate", "cli", "cpp11", "DelayedArray", "dplyr", "farver", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "openxlsx", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "Rcpp", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector", "zip" ], "_vignettes": [ { "source": "CalibraCurve.Rmd", "filename": "CalibraCurve.html", "title": "Introduction to CalibraCurve", "author": "Karin Schork", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation of CalibraCurve", "Asking for help", "Citing CalibraCurve", "Quick start to using CalibraCurve", "Example data set", "Import one or more xlsx, csv or txt files", "Import SummarizedExperiments object", "Apply CalibraCurve", "Use calibration curve for prediction", "Further information", "Comparison with other related packages", "R session information", "Bibliography" ], "created": "2025-10-02 07:58:38", "modified": "2025-10-02 15:07:56", "commits": 5 }, { "source": "CalibraCurve_Visualization.Rmd", "filename": "CalibraCurve_Visualization.html", "title": "Customizing the visualizations of CalibraCurve", "author": "Karin Schork", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Handling multiple calibration curves", "Multiplot", "All-in-one plot", "Changing colours", "Other plot elements", "R session information", "Bibliography" ], "created": "2025-07-30 11:09:02", "modified": "2025-10-02 14:16:43", "commits": 2 } ], "_score": 6.380211241711606, "_indexed": true, "_nocasepkg": "calibracurve", "_universes": [ "bioc", "karinschork", "mpc-bioinformatics" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-05-31T06:44:55.000Z", "distro": "noble", "commit": "7140fc647bf03fcfe2ace98eb66a1d59181d380a", "fileid": "78ae7a529d29ed34e8def50c4e22480ec374d290d41537d375dae7e3f5fdbb9b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705548278" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-05-31T06:44:16.000Z", "distro": "noble", "commit": "7140fc647bf03fcfe2ace98eb66a1d59181d380a", "fileid": "d88d5799348de2fbd392bb52df2400eae6b0e3be78aae77f854965b1a9e90a6e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705548278" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-05-31T07:43:32.000Z", "commit": "7140fc647bf03fcfe2ace98eb66a1d59181d380a", "fileid": "42bca4a60715a8b94204a28076032d9b7da9f9508cfbd3b764a467579db60f12", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705548278" }, { "r": "4.6.0", "os": "mac", "version": "1.3.0", "date": "2026-05-31T07:43:23.000Z", "commit": "7140fc647bf03fcfe2ace98eb66a1d59181d380a", "fileid": "684a3b4e5e4dd47f1bb48584644fe2a683098d45fac663e80b6cb8b161bd8008", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705548278" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-05-31T06:44:08.000Z", "commit": "7140fc647bf03fcfe2ace98eb66a1d59181d380a", "fileid": "fa1c76375fc13a14ceb4a94813a9b9c180922e38d4aee27051548a951abbeaee", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705548278" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-05-31T06:43:10.000Z", "commit": "7140fc647bf03fcfe2ace98eb66a1d59181d380a", "fileid": "5ada63f5eb3fb6041a0147e3548777131d33b3d0f9f1ed078c45c48e287ab080", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705548278" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-05-31T06:44:07.000Z", "commit": "7140fc647bf03fcfe2ace98eb66a1d59181d380a", "fileid": "e09e6c084d1bf8dd3acfd4881970228821032f686885b21714930297fe7e4416", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705548278" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-05-31T06:43:18.000Z", "commit": "7140fc647bf03fcfe2ace98eb66a1d59181d380a", "fileid": "837955da5d3c4db2690ef3d423a9bfe8c14f2c2ff373de492ce7de2ac88eaf06", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705548278" } ] }