Package: patRoon Type: Package Title: Workflows for Mass-Spectrometry Based Non-Target Analysis Version: 3.0.0 Authors@R: c( person("Rick", "Helmus", email = "r.helmus@uva.nl", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9401-3133") ), person("Olaf", "Brock", role = "ctb", comment = c(ORCID = "0000-0003-4727-8459") ), person("Vittorio", "Albergamo", role = "ctb", comment = c(ORCID = "0000-0002-5347-1362") ), person("Andrea", "Brunner", role = "ctb", comment = c(ORCID = "0000-0002-2801-1751") ), person("Emma", "Schymanski", role = "ctb", comment = c(ORCID = "0000-0001-6868-8145") ), person("Bas", "van de Velde", role = "ctb", comment = c(ORCID = "0000-0003-1292-3251"), ), person("Leon", "Saal", role = "ctb", comment = c(ORCID = "0000-0002-3522-7729"), )) Description: Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting. License: GPL-3 URL: https://github.com/rickhelmus/patRoon BugReports: https://github.com/rickhelmus/patRoon/issues Encoding: UTF-8 Depends: R (>= 4.1.0) SystemRequirements: GNU make Imports: methods, checkmate (>= 1.8.5), Rcpp, VennDiagram, UpSetR, stats, utils, parallel, grid, graphics, RColorBrewer, data.table (>= 1.15.0), withr, digest, DBI, RSQLite (>= 2.2.4), fst, processx, tools, MSnbase, Biobase, BiocParallel, xcms, cluster, fastcluster, gplots, heatmaply, dynamicTreeCut, dendextend, igraph, visNetwork, rJava, rcdk, fingerprint, mzR, circlize, miniUI, rhandsontable, rstudioapi, htmlwidgets, shiny, shinyjs, CAMERA, enviPat, knitr, rmarkdown, bslib (>= 0.9.0), bsicons, reactable (>= 0.4.1), magrittr, kableExtra, R.utils, magick, glue, jsonlite, Rdpack, rsm, future, future.apply, fs, yaml, keys, backports, httr, getPass, lzstring, constructive, signal, MBA Suggests: RDCOMClient, metfRag, enviPick, nontarget, RAMClustR, cliqueMS, KPIC, MetaClean, MetaCleanData, testthat, rlang, vdiffr, patRoonData, devtools, covr, DiagrammeR, DiagrammeRsvg, rsvg, pkgload, splashR, MS2Quant, MS2Tox, ChemmineR, fmcsR, reticulate, Rmstoolkitlib LinkingTo: Rcpp, rapidjsonr Config/testthat/edition: 3 Config/testthat/parallel: true Config/testthat/start-first: feature*, screening, compounds, components, tp, formulas, pred, mspeaklists, project-tool, report RdMacros: Rdpack Collate: 'RcppExports.R' 'generics.R' 'cache.R' 'main.R' 'workflow-step.R' 'TP.R' 'TP-structure.R' 'TP-CTS.R' 'TP-ann_comp.R' 'TP-formula.R' 'TP-ann_form.R' 'TP-biotransformer.R' 'TP-library.R' 'TP-library_formula.R' 'features.R' 'workflow-step-set.R' 'features-set.R' 'feature_groups.R' 'feature_groups-set.R' 'TP-logic.R' 'utils.R' 'utils-adduct.R' 'adduct.R' 'analysisInfo.R' 'check_ui.R' 'utils-components.R' 'components.R' 'check_components.R' 'check_features.R' 'components-camera.R' 'components-features.R' 'components-cliquems.R' 'components-clust.R' 'components-intclust.R' 'components-set.R' 'components-nontarget.R' 'components-nontarget-set.R' 'components-openms.R' 'components-ramclustr.R' 'components-specclust.R' 'feature_annotations.R' 'formulas.R' 'mspeaklists.R' 'compounds.R' 'utils-compounds.R' 'utils-screening.R' 'feature_groups-screening.R' 'feature_groups-screening-set.R' 'components-tps.R' 'compounds-cluster.R' 'mslibrary.R' 'compounds-library.R' 'compounds-metfrag.R' 'utils-feat_annotations-set.R' 'compounds-set.R' 'utils-sirius.R' 'compounds-sirius.R' 'convert.R' 'defunct.R' 'utils-bruker.R' 'deprecated-formulas-bruker.R' 'deprecated-mspeaklists-bruker.R' 'deprecated-mspeaklists-mzr.R' 'deprecated.R' 'utils-IPO.R' 'doe-optimizer.R' 'eic_eim_gui.R' 'feature_groups-ADT.R' 'feature_groups-bruker.R' 'feature_groups-comparison.R' 'feature_groups-envimass.R' 'feature_groups-filter.R' 'feature_groups-greedy.R' 'feature_groups-ims.R' 'feature_groups-kpic2.R' 'feature_groups-openms.R' 'feature_groups-optimize.R' 'feature_groups-optimize-kpic2.R' 'feature_groups-optimize-openms.R' 'feature_groups-optimize-xcms.R' 'feature_groups-optimize-xcms3.R' 'feature_groups-plot.R' 'feature_groups-sirius.R' 'feature_groups-table.R' 'feature_groups-tasq.R' 'feature_groups-xcms.R' 'feature_groups-xcms3.R' 'features-bruker.R' 'features-envipick.R' 'features-kpic2.R' 'features-openms.R' 'features-optimize.R' 'features-optimize-envipick.R' 'features-optimize-kpic2.R' 'features-optimize-openms.R' 'features-optimize-xcms.R' 'features-optimize-xcms3.R' 'features-piek.R' 'features-safd.R' 'features-sirius.R' 'features-table.R' 'features-tasq.R' 'features-xcms.R' 'features-xcms3.R' 'formulas-genform.R' 'formulas-set.R' 'formulas-sirius.R' 'limits.R' 'msdata.R' 'mslibrary-json.R' 'mslibrary-msp.R' 'mspeaklists-set.R' 'multi-process-classic.R' 'multi-process-future.R' 'multi-process.R' 'peaks.R' 'project-tool-analyses.R' 'project-tool-annotation.R' 'project-tool-features.R' 'project-tool-gen.R' 'project-tool-general.R' 'project-tool-pre_treatment.R' 'project-tool-report.R' 'project-tool-tp.R' 'project-tool-utils.R' 'project-tool.R' 'report-html.R' 'report-html-TPs.R' 'report-html-components.R' 'report-html-feat_annotations.R' 'report-html-features.R' 'report-html-utils.R' 'report-legacy.R' 'report.R' 'utils-TPs.R' 'utils-checkmate.R' 'utils-exported.R' 'utils-feat_annotations.R' 'utils-features-ims.R' 'utils-features-sets.R' 'utils-features.R' 'utils-formulas.R' 'utils-mol.R' 'utils-msdata.R' 'utils-mslibrary.R' 'utils-mspeaklists.R' 'utils-optimize.R' 'utils-plot.R' 'utils-progress.R' 'utils-sets.R' 'utils-xcms.R' 'zzz.R' VignetteBuilder: knitr Config/roxygen2/version: 8.0.0 Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev libfribidi-dev libglpk-dev make libharfbuzz-dev libmagick++-dev gsfonts default-jdk libicu-dev libpng-dev libuv1-dev libxml2-dev libnetcdf-dev libssl-dev zlib1g-dev Repository: https://rickhelmus.r-universe.dev Date/Publication: 2026-06-26 13:58:27 UTC RemoteUrl: https://github.com/rickhelmus/patRoon RemoteRef: HEAD RemoteSha: e0e23ddc5c380ae27b0433c6d25c402c0d3529d8 NeedsCompilation: yes Packaged: 2026-06-26 16:25:29 UTC; root Author: Rick Helmus [aut, cre] (ORCID: ), Olaf Brock [ctb] (ORCID: ), Vittorio Albergamo [ctb] (ORCID: ), Andrea Brunner [ctb] (ORCID: ), Emma Schymanski [ctb] (ORCID: ), Bas van de Velde [ctb] (ORCID: ), Leon Saal [ctb] (ORCID: ) Maintainer: Rick Helmus