{ "_id": "6a1fdc77b401979e734380a8", "Package": "peakPantheR", "Title": "Peak Picking and Annotation of High Resolution Experiments", "Version": "1.27.0", "Date": "2025-09-27", "Authors@R": "c(person(\"Arnaud\", \"Wolfer\", email = \"adwolfer@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5856-3218\")),\nperson(\"Goncalo\", \"Correia\", email = \"gscorreia89@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-8271-9294\")),\nperson(\"Jake\", \"Pearce\", email = \"jake.pearce@gmail.com\", role = \"ctb\"),\nperson(\"Caroline\", \"Sands\", email = \"caz119@hotmail.co.uk\", role = \"ctb\"))", "Description": "An automated pipeline for the detection, integration and\nreporting of predefined features across a large number of mass\nspectrometry data files. It enables the real time annotation of\nmultiple compounds in a single file, or the parallel annotation\nof multiple compounds in multiple files. A graphical user\ninterface as well as command line functions will assist in\nassessing the quality of annotation and update fitting\nparameters until a satisfactory result is obtained.", "biocViews": "MassSpectrometry, Metabolomics, PeakDetection", "License": "GPL-3", "BugReports": "https://github.com/phenomecentre/peakPantheR/issues/new", "URL": "https://github.com/phenomecentre/peakPantheR", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev libglpk-dev make libharfbuzz-dev libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libnetcdf-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:51:00 UTC", "RemoteUrl": "https://github.com/bioc/peakPantheR", "RemoteRef": "HEAD", "RemoteSha": "efe437366d3cc0b38e5ec2d5de8ca9c00ed0114c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 07:26:32 UTC", "User": "root" }, "Author": "Arnaud Wolfer [aut, cre] (ORCID:\n),\nGoncalo Correia [aut] (ORCID: ),\nJake Pearce [ctb],\nCaroline Sands [ctb]", "Maintainer": "Arnaud Wolfer ", "MD5sum": "041f99aded9750bdc4e6b43d088b28d3", "_user": "bioc", "_type": "src", "_file": "peakPantheR_1.27.0.tar.gz", "_fileid": "7245df9bc060bf153e368b3f629cef514266fd841f485c84279c26cc1fd23de5", "_filesize": 3592715, "_sha256": "7245df9bc060bf153e368b3f629cef514266fd841f485c84279c26cc1fd23de5", "_created": "2026-06-03T07:26:32.000Z", "_published": "2026-06-03T07:49:11.202Z", "_jobs": [ { "job": 79243187701, "time": 229, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7378302797" }, { "job": 79243187707, "time": 1202, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7378614237" }, { "job": 79243187710, "time": 1291, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7378645220" }, { "job": 79243187732, "time": 700, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7378454154" }, { "job": 79243187671, "time": 881, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7378515633" }, { "job": 79242309942, "time": 363, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7378234562" }, { "job": 79243187731, "time": 229, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7378303222" }, { "job": 79243187750, "time": 1286, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7378643899" }, { "job": 79243187765, "time": 1308, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7378653437" }, { "job": 79243187760, "time": 1231, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7378625742" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26869864796", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/peakPantheR", "_commit": { "id": "efe437366d3cc0b38e5ec2d5de8ca9c00ed0114c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380660 }, "_maintainer": { "name": "Arnaud Wolfer", "email": "adwolfer@gmail.com", "login": "adwolfer", "orcid": "0000-0001-5856-3218", "description": "", "uuid": 7688243 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5", "role": "Depends" }, { "package": "foreach", "version": ">= 1.4.4", "role": "Imports" }, { "package": "doParallel", "version": ">= 1.0.11", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.5.0", "role": "Imports" }, { "package": "gridExtra", "version": ">= 2.3", "role": "Imports" }, { "package": "MSnbase", "version": ">= 2.4.0", "role": "Imports" }, { "package": "mzR", "version": ">= 2.12.0", "role": "Imports" }, { "package": "stringr", "version": ">= 1.2.0", "role": "Imports" }, { "package": "methods", "version": ">= 3.4.0", "role": "Imports" }, { "package": "XML", "version": ">= 3.98.1.10", "role": "Imports" }, { "package": "minpack.lm", "version": ">= 1.2.1", "role": "Imports" }, { "package": "scales", "version": ">= 0.5.0", "role": "Imports" }, { "package": "shiny", "version": ">= 1.0.5", "role": "Imports" }, { "package": "bslib", "role": "Imports" }, { "package": "shinycssloaders", "version": ">= 1.0.0", "role": "Imports" }, { "package": "DT", "version": ">= 0.15", "role": "Imports" }, { "package": "pracma", "version": ">= 2.2.3", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "lubridate", "role": "Imports" }, { "package": "svglite", "version": ">= 2.1.1", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "faahKO", "role": "Suggests" }, { "package": "msdata", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "pander", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-39", "n": 4 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23" } ], "_topics": [ "massspectrometry", "metabolomics", "peakdetection", "feature-detection", "mass-spectrometry" ], "_stars": 13, "_contributors": [ { "user": "adwolfer", "count": 452, "uuid": 7688243 }, { "user": "gscorreia89", "count": 56, "uuid": 4366393 }, { "user": "nturaga", "count": 12, "uuid": 2746443 }, { "user": "jaketmp", "count": 12, "uuid": 738903 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 318, "source": "https://www.bioconductor.org/packages/stats/bioc/peakPantheR" }, "_devurl": "https://github.com/phenomecentre/peakpanther", "_searchresults": 46, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/peakPantheR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/phenomecentre/peakpanther", "_realowner": "bioc", "_cranurl": false, "_releases": [ { "version": "1.2.0", "date": "2018-07-10" } ], "_exports": [ "acquisitionTime", "annotation_diagnostic_multiplot_UI_helper", "annotation_fit_summary_UI_helper", "annotation_showMethod_UI_helper", "annotation_showText_UI_helper", "annotationDiagnosticPlots", "annotationParamsDiagnostic", "annotationTable", "cpdID", "cpdMetadata", "cpdName", "dataPoints", "EICs", "filename", "filepath", "FIR", "initialise_annotation_from_files_UI_helper", "isAnnotated", "load_annotation_from_file_UI_helper", "nbCompounds", "nbSamples", "outputAnnotationDiagnostic", "outputAnnotationFeatureMetadata_UI_helper", "outputAnnotationParamsCSV", "outputAnnotationResult", "outputAnnotationSpectraMetadata_UI_helper", "peakFit", "peakPantheR_loadAnnotationParamsCSV", "peakPantheR_parallelAnnotation", "peakPantheR_plotEICFit", "peakPantheR_plotPeakwidth", "peakPantheR_quickEIC", "peakPantheR_ROIStatistics", "peakPantheR_singleFileSearch", "peakPantheR_start_GUI", "peakPantheRAnnotation", "peakTables", "resetAnnotation", "resetFIR", "retentionTimeCorrection", "ROI", "spectra_metadata_colourScheme_UI_helper", "spectraMetadata", "spectraPaths_and_metadata_UI_helper", "TIC", "uROI", "uROIExist", "useFIR", "useUROI" ], "_help": [ { "page": "sub-peakPantheRAnnotation-ANY-ANY-ANY-method", "title": "extract parts of peakPantheRAnnotation class", "topics": [ "[,peakPantheRAnnotation,ANY,ANY,ANY-method", "[,peakPantheRAnnotation-method" ] }, { "page": "acquisitionTime-peakPantheRAnnotation-method", "title": "acquisitionTime accessor returns value as.POSIXct", "topics": [ "acquisitionTime", "acquisitionTime,peakPantheRAnnotation-method" ] }, { "page": "annotation_diagnostic_multiplot_UI_helper", "title": "UI diagnostic plot helper - single feature multiplot", "topics": [ "annotation_diagnostic_multiplot_UI_helper" ] }, { "page": "annotation_fit_summary_UI_helper", "title": "UI diagnostic table - fit summary", "topics": [ "annotation_fit_summary_UI_helper" ] }, { "page": "annotation_showMethod_UI_helper", "title": "UI show annotation helper - list of properties", "topics": [ "annotation_showMethod_UI_helper" ] }, { "page": "annotation_showText_UI_helper", "title": "UI show annotation helper - UI sidebar string", "topics": [ "annotation_showText_UI_helper" ] }, { "page": "annotationDiagnosticMultiplot", "title": "Generate a multiplot of all diagnostic plots", "topics": [ "annotationDiagnosticMultiplot" ] }, { "page": "annotationDiagnosticPlots-peakPantheRAnnotation-method", "title": "Generate fit diagnostic plots", "topics": [ "annotationDiagnosticPlots", "annotationDiagnosticPlots,peakPantheRAnnotation-method" ] }, { "page": "annotationParamsDiagnostic-peakPantheRAnnotation-method", "title": "Set uROI and FIR based on annotation results", "topics": [ "annotationParamsDiagnostic", "annotationParamsDiagnostic,peakPantheRAnnotation-method" ] }, { "page": "annotationTable-peakPantheRAnnotation-method", "title": "annotationTable accessor", "topics": [ "annotationTable", "annotationTable,peakPantheRAnnotation-method" ] }, { "page": "cpdID-peakPantheRAnnotation-method", "title": "cpdID accessor", "topics": [ "cpdID", "cpdID,peakPantheRAnnotation-method" ] }, { "page": "cpdMetadata-peakPantheRAnnotation-method", "title": "cpdMetadata accessor", "topics": [ "cpdMetadata", "cpdMetadata,peakPantheRAnnotation-method" ] }, { "page": "cpdName-peakPantheRAnnotation-method", "title": "cpdName accessor", "topics": [ "cpdName", "cpdName,peakPantheRAnnotation-method" ] }, { "page": "dataPoints-peakPantheRAnnotation-method", "title": "dataPoints accessor", "topics": [ "dataPoints", "dataPoints,peakPantheRAnnotation-method" ] }, { "page": "EICs-peakPantheRAnnotation-method", "title": "EICs accessor", "topics": [ "EICs", "EICs,peakPantheRAnnotation-method" ] }, { "page": "emgGaussian_guess", "title": "Guess function for initial exponentially modified gaussian parameters and bounds", "topics": [ "emgGaussian_guess" ] }, { "page": "emgGaussian_minpack.lm", "title": "Implementation of the Exponentially Modified Gaussian (EMG) peak shape for use with minpack.lm", "topics": [ "emgGaussian_minpack.lm" ] }, { "page": "emgGaussian_minpack.lm_objectiveFun", "title": "Exponentially Modified Gaussian minpack.lm objective function", "topics": [ "emgGaussian_minpack.lm_objectiveFun" ] }, { "page": "extractSignalRawData", "title": "Extract signal in a multiple defined mz rt window from a raw data file", "topics": [ "extractSignalRawData" ] }, { "page": "filename-peakPantheRAnnotation-method", "title": "filename accessor by spliting filepath", "topics": [ "filename", "filename,peakPantheRAnnotation-method" ] }, { "page": "filepath-peakPantheRAnnotation-method", "title": "filepath accessor", "topics": [ "filepath", "filepath,peakPantheRAnnotation-method" ] }, { "page": "findTargetFeatures", "title": "Find and integrate target features in each ROI", "topics": [ "findTargetFeatures" ] }, { "page": "FIR-peakPantheRAnnotation-method", "title": "FIR accessor returns targetFeatTable with cpdID, cpdName added", "topics": [ "FIR", "FIR,peakPantheRAnnotation-method" ] }, { "page": "fitCurve", "title": "Curve fitting using minpack.lm", "topics": [ "fitCurve" ] }, { "page": "gaussian_cerf", "title": "Gaussian Error function", "topics": [ "gaussian_cerf" ] }, { "page": "gaussian_erf", "title": "Gaussian Error function", "topics": [ "gaussian_erf" ] }, { "page": "generateIonChromatogram", "title": "Generate ion chromatogram from raw data points", "topics": [ "generateIonChromatogram" ] }, { "page": "getAcquisitionDatemzML", "title": "Parse acquisition date from a mzML file", "topics": [ "getAcquisitionDatemzML" ] }, { "page": "getTargetFeatureStatistic", "title": "Calculate chromatographic peak properties", "topics": [ "getTargetFeatureStatistic" ] }, { "page": "initialise_annotation_from_files_UI_helper", "title": "UI data import helper - initialise new annotation from files", "topics": [ "initialise_annotation_from_files_UI_helper" ] }, { "page": "integrateFIR", "title": "Integrate fallback integration regions", "topics": [ "integrateFIR" ] }, { "page": "is.peakPantheR_curveFit", "title": "Check if object is of class peakPantheR_curveFit", "topics": [ "is.peakPantheR_curveFit" ] }, { "page": "isAnnotated-peakPantheRAnnotation-method", "title": "isAnnotated accessor", "topics": [ "isAnnotated", "isAnnotated,peakPantheRAnnotation-method" ] }, { "page": "load_annotation_from_file_UI_helper", "title": "UI data import helper - check loaded annotation", "topics": [ "load_annotation_from_file_UI_helper" ] }, { "page": "nbCompounds-peakPantheRAnnotation-method", "title": "nbCompounds accessor established on cpdID", "topics": [ "nbCompounds", "nbCompounds,peakPantheRAnnotation-method" ] }, { "page": "nbSamples-peakPantheRAnnotation-method", "title": "nbSamples accessor established on filepath", "topics": [ "nbSamples", "nbSamples,peakPantheRAnnotation-method" ] }, { "page": "outputAnnotationDiagnostic-peakPantheRAnnotation-method", "title": "Save to disk the annotation parameters as CSV and a diagnostic plot per fitted compound", "topics": [ "outputAnnotationDiagnostic", "outputAnnotationDiagnostic,peakPantheRAnnotation-method" ] }, { "page": "outputAnnotationFeatureMetadata_UI_helper", "title": "UI export helper - feature metadata", "topics": [ "outputAnnotationFeatureMetadata_UI_helper" ] }, { "page": "outputAnnotationParamsCSV-peakPantheRAnnotation-method", "title": "Save annotation parameters as CSV", "topics": [ "outputAnnotationParamsCSV", "outputAnnotationParamsCSV,peakPantheRAnnotation-method" ] }, { "page": "outputAnnotationResult-peakPantheRAnnotation-method", "title": "Save to disk all annotation results as csv files", "topics": [ "outputAnnotationResult", "outputAnnotationResult,peakPantheRAnnotation-method" ] }, { "page": "outputAnnotationSpectraMetadata_UI_helper", "title": "UI export helper - spectra path and metadata", "topics": [ "outputAnnotationSpectraMetadata_UI_helper" ] }, { "page": "peakFit-peakPantheRAnnotation-method", "title": "peakFit accessor", "topics": [ "peakFit", "peakFit,peakPantheRAnnotation-method" ] }, { "page": "peakPantheR", "title": "peakPantheR: A package for Peak Picking and ANnoTation of High resolution Experiments", "topics": [ "peakPantheR-package", "peakPantheR" ] }, { "page": "peakPantheR_applyRTCorrection", "title": "Correct targeted retention time based on reference compounds", "topics": [ "peakPantheR_applyRTCorrection" ] }, { "page": "peakPantheR_loadAnnotationParamsCSV", "title": "Load fit parameters from CSV", "topics": [ "peakPantheR_loadAnnotationParamsCSV" ] }, { "page": "peakPantheR_parallelAnnotation", "title": "Search, integrate and report targeted features in a multiple spectra", "concept": [ "parallelAnnotation", "peakPantheR" ], "topics": [ "peakPantheR_parallelAnnotation" ] }, { "page": "peakPantheR_plotEICFit", "title": "Plot samples raw data and detected feature for a single ROI", "topics": [ "peakPantheR_plotEICFit" ] }, { "page": "peakPantheR_plotPeakwidth", "title": "Plot peak value and peakwidth by acquisition time or in input order", "topics": [ "peakPantheR_plotPeakwidth" ] }, { "page": "peakPantheR_quickEIC", "title": "Extract and plot a EIC from a raw data file", "topics": [ "peakPantheR_quickEIC" ] }, { "page": "peakPantheR_ROIStatistics", "title": "Save to disk each ROI EIC and mean IS RT", "topics": [ "peakPantheR_ROIStatistics" ] }, { "page": "peakPantheR_singleFileSearch", "title": "Search, integrate and report targeted features in a raw spectra", "concept": [ "parallelAnnotation", "peakPantheR", "realTimeAnnotation" ], "topics": [ "peakPantheR_singleFileSearch" ] }, { "page": "peakPantheR_start_GUI", "title": "peakPantheR Graphical User Interface", "topics": [ "peakPantheR_start_GUI" ] }, { "page": "peakPantheRAnnotation", "title": "An S4 class to represent peakPantheR annotation results", "concept": [ "parallelAnnotation", "peakPantheR" ], "topics": [ "peakPantheRAnnotation", "peakPantheRAnnotation-class" ] }, { "page": "peakTables-peakPantheRAnnotation-method", "title": "peakTables accessor with cpdID and cpdName added back", "topics": [ "peakTables", "peakTables,peakPantheRAnnotation-method" ] }, { "page": "plotEICDetectedPeakwidth", "title": "Plot samples raw data and detected feature for a single ROI", "topics": [ "plotEICDetectedPeakwidth" ] }, { "page": "plotHistogram", "title": "Plot variable histogram and density", "topics": [ "plotHistogram" ] }, { "page": "predictCurve", "title": "Predict curve values", "topics": [ "predictCurve" ] }, { "page": "prepare_advanced_target_parameters", "title": "Process target region parameters (with uROI, FIR) for object initialisation", "topics": [ "prepare_advanced_target_parameters" ] }, { "page": "prepare_basic_target_parameters", "title": "Process target region parameters (simple format) for object initialisation", "topics": [ "prepare_basic_target_parameters" ] }, { "page": "resetAnnotation-peakPantheRAnnotation-method", "title": "Reset a peakPantheRAnnotation and alter samples and compounds information", "topics": [ "resetAnnotation", "resetAnnotation,peakPantheRAnnotation-method" ] }, { "page": "resetFIR-peakPantheRAnnotation-method", "title": "Reset FIR windows to uROI or ROI values Reset FIR windows to uROI (or ROI if 'uROIExist=FALSE')", "topics": [ "resetFIR", "resetFIR,peakPantheRAnnotation-method" ] }, { "page": "retentionTimeCorrection-peakPantheRAnnotation-method", "title": "Apply retention time correction methods to adjust the retention time information in the uROI of peakPantheRAnnotation object", "topics": [ "retentionTimeCorrection", "retentionTimeCorrection,peakPantheRAnnotation-method" ] }, { "page": "ROI-peakPantheRAnnotation-method", "title": "ROI accessor returns targetFeatTable with cpdID, cpdName added", "topics": [ "ROI", "ROI,peakPantheRAnnotation-method" ] }, { "page": "saveSingleFileMultiEIC", "title": "Save to disk a plot of all ROI EIC and detected feature range", "topics": [ "saveSingleFileMultiEIC" ] }, { "page": "skewedGaussian_guess", "title": "Guess function for initial skewed gaussian parameters and bounds", "topics": [ "skewedGaussian_guess" ] }, { "page": "skewedGaussian_minpack.lm", "title": "Implementation of the Skewed Gaussian peak shape for use with minpack.lm", "topics": [ "skewedGaussian_minpack.lm" ] }, { "page": "skewedGaussian_minpack.lm_objectiveFun", "title": "Skewed Gaussian minpack.lm objective function", "topics": [ "skewedGaussian_minpack.lm_objectiveFun" ] }, { "page": "spectra_metadata_colourScheme_UI_helper", "title": "UI export plot helper - sample colour", "topics": [ "spectra_metadata_colourScheme_UI_helper" ] }, { "page": "spectraMetadata-peakPantheRAnnotation-method", "title": "spectraMetadata accessor", "topics": [ "spectraMetadata", "spectraMetadata,peakPantheRAnnotation-method" ] }, { "page": "spectraPaths_and_metadata_UI_helper", "title": "UI data import helper - prepare file paths and metadata", "topics": [ "spectraPaths_and_metadata_UI_helper" ] }, { "page": "TIC-peakPantheRAnnotation-method", "title": "TIC accessor", "topics": [ "TIC", "TIC,peakPantheRAnnotation-method" ] }, { "page": "uROI-peakPantheRAnnotation-method", "title": "uROI accessor returns targetFeatTable with cpdID, cpdName added", "topics": [ "uROI", "uROI,peakPantheRAnnotation-method" ] }, { "page": "uROIExist-peakPantheRAnnotation-method", "title": "uROIExist accessor", "topics": [ "uROIExist", "uROIExist,peakPantheRAnnotation-method" ] }, { "page": "useFIR-peakPantheRAnnotation-method", "title": "useFIR accessor", "topics": [ "useFIR", "useFIR,peakPantheRAnnotation-method" ] }, { "page": "useUROI-peakPantheRAnnotation-method", "title": "useUROI accessor", "topics": [ "useUROI", "useUROI,peakPantheRAnnotation-method" ] } ], "_readme": "https://github.com/bioc/peakPantheR/raw/HEAD/README.md", "_rundeps": [ "abind", "affy", "affyio", "AnnotationFilter", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "biocmake", "BiocManager", "BiocParallel", "bslib", "cachem", "cli", "clue", "cluster", "codetools", "commonmark", "cpp11", "crosstalk", "curl", "data.table", "DelayedArray", "digest", "dir.expiry", "doParallel", "dplyr", "DT", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "igraph", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "lubridate", "magrittr", "MALDIquant", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "MetaboCoreUtils", "mime", "minpack.lm", "MsCoreUtils", "MSnbase", "MultiAssayExperiment", "mzID", "mzR", "ncdf4", "openssl", "otel", "pcaMethods", "pillar", "pkgconfig", "plotly", "plyr", "pracma", "preprocessCore", "promises", "ProtGenerics", "PSMatch", "PTMods", "purrr", "QFeatures", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "Rhdf5lib", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "shiny", "shinycssloaders", "snow", "sourcetools", "SparseArray", "Spectra", "statmod", "stringi", "stringr", "SummarizedExperiment", "svglite", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "timechange", "tinytex", "utf8", "vctrs", "viridisLite", "vsn", "withr", "xfun", "XML", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "getting-started.Rmd", "filename": "getting-started.html", "title": "Getting Started with the peakPantheR package", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Installation", "Getting Started", "Input Data", "MS files", "Expected regions of interest", "Preparing input for the graphical user interface", "peakPantheRAnnotation .RData", "CSV file input", "Targeted features", "Files to process and spectra metadata (optional)", "Feature meatadata (optional)", "See Also", "Session Information", "References" ], "created": "2018-02-26 16:48:10", "modified": "2025-09-27 22:20:09", "commits": 12 }, { "source": "parallel-annotation.Rmd", "filename": "parallel-annotation.html", "title": "Parallel Annotation", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Abbreviations", "Parallel Annotation Concept", "Parallel Annotation Example", "Input Data", "Initialise and Run Parallel Annotation", "Process Parallel Annotation Results", "Retention time correction", "New Initialisation with Updated Parameters to be Applied to All Study Samples", "Load new fit parameters", "Add new samples to process", "Run Final Parallel Annotation", "Output final results", "See Also", "Session Information" ], "created": "2018-02-26 16:48:10", "modified": "2025-09-27 22:20:09", "commits": 13 }, { "source": "peakPantheR-GUI.Rmd", "filename": "peakPantheR-GUI.html", "title": "peakPantheR Graphical User Interface", "author": "Arnaud Wolfer", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Abbreviations", "Example Data", "Getting Started", "Graphical User Interface", "Import", "Run Annotation", "Diagnostic: plot & update", "View results", "Export", "Final Note", "See Also", "Session Information" ], "created": "2020-10-13 14:18:19", "modified": "2025-09-27 22:20:09", "commits": 4 }, { "source": "real-time-annotation.Rmd", "filename": "real-time-annotation.html", "title": "Real Time Annotation", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Abbreviations", "Real Time Annotation Concept", "Real Time Annotation Example", "Input Data", "Run Single File Annotation", "See Also", "Session Information" ], "created": "2018-02-26 16:48:10", "modified": "2025-09-27 22:20:09", "commits": 12 } ], "_score": 7.156912425700018, "_indexed": true, "_nocasepkg": "peakpanther", "_universes": [ "bioc", "adwolfer", "phenomecentre" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.27.0", "date": "2026-06-03T07:30:49.000Z", "distro": "noble", "commit": "efe437366d3cc0b38e5ec2d5de8ca9c00ed0114c", "fileid": "5568c5e8d033bbccfd14af8299c1492b074b67c288f03913b7f48ce2401e819b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26869864796" }, { "r": "4.6.0", "os": "linux", "version": "1.27.0", "date": "2026-06-03T07:31:02.000Z", "distro": "noble", "commit": "efe437366d3cc0b38e5ec2d5de8ca9c00ed0114c", "fileid": "1f9cce2d4a23b236671945088c52a9fa675cdf41ec95e90b5360689da4553d13", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26869864796" }, { "r": "4.5.3", "os": "mac", "version": "1.27.0", "date": "2026-06-03T07:29:06.000Z", "commit": "efe437366d3cc0b38e5ec2d5de8ca9c00ed0114c", "fileid": "30800102fd3c3406c37d38185939b9b10c9e2e682deefb868809fd86eedc2e56", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26869864796" }, { "r": "4.6.0", "os": "mac", "version": "1.27.0", "date": "2026-06-03T07:29:20.000Z", "commit": "efe437366d3cc0b38e5ec2d5de8ca9c00ed0114c", "fileid": "7c9d1ca3ce02d6707a4a9b21986539c325d7a4fcce7dcc2e2b5505037f336af7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26869864796" }, { "r": "4.6.0", "os": "wasm", "version": "1.27.0", "date": "2026-06-03T07:30:46.000Z", "commit": "efe437366d3cc0b38e5ec2d5de8ca9c00ed0114c", "fileid": "675a7626de8c6626e2e1e5a37b26432493755b9e0de01df990ae4b55a90d58ed", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26869864796" }, { "r": "4.7.0", "os": "win", "version": "1.27.0", "date": "2026-06-03T07:31:30.000Z", "commit": "efe437366d3cc0b38e5ec2d5de8ca9c00ed0114c", "fileid": "a11f88221b32b55b3da81bcac8b8b363860bd2aa271aab783c51f3dd0b2b5dfe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26869864796" }, { "r": "4.5.3", "os": "win", "version": "1.27.0", "date": "2026-06-03T07:31:44.000Z", "commit": "efe437366d3cc0b38e5ec2d5de8ca9c00ed0114c", "fileid": "7341acc13a262c0eb854d4b1666e962830d0d1d782bc7c7423dc4c9daaee3702", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26869864796" }, { "r": "4.6.0", "os": "win", "version": "1.27.0", "date": "2026-06-03T07:31:29.000Z", "commit": "efe437366d3cc0b38e5ec2d5de8ca9c00ed0114c", "fileid": "9a6c450e930b4639be011aec8ad7cf62b9eb8876400c2ef8b9411a344f88d562", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26869864796" } ] }