Files in rickhelmus/patRoon

Workflows for Mass-Spectrometry Based Non-Target Analysis

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DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/RcppExports.R R/TP-CTS.R R/TP-biotransformer.R R/TP-formula.R R/TP-library.R R/TP-library_formula.R R/TP-logic.R R/TP-structure.R R/TP.R R/adduct.R R/analysisInfo.R R/cache.R R/check_components.R R/check_features.R R/check_ui.R R/components-camera.R R/components-cliquems.R R/components-clust.R R/components-features.R R/components-intclust.R R/components-nontarget-set.R R/components-nontarget.R R/components-openms.R R/components-ramclustr.R R/components-set.R R/components-specclust.R R/components-tps.R R/components.R R/compounds-cluster.R R/compounds-library.R R/compounds-metfrag.R R/compounds-set.R R/compounds-sirius.R R/compounds.R R/convert.R R/defunct.R R/deprecated.R R/doe-optimizer.R R/feature_annotations.R R/feature_groups-bruker.R R/feature_groups-comparison.R R/feature_groups-envimass.R R/feature_groups-filter.R R/feature_groups-kpic2.R R/feature_groups-openms.R R/feature_groups-optimize-kpic2.R R/feature_groups-optimize-openms.R R/feature_groups-optimize-xcms.R R/feature_groups-optimize-xcms3.R R/feature_groups-optimize.R R/feature_groups-plot.R R/feature_groups-screening-set.R R/feature_groups-screening.R R/feature_groups-set.R R/feature_groups-sirius.R R/feature_groups-tasq.R R/feature_groups-xcms.R R/feature_groups-xcms3.R R/feature_groups.R R/features-bruker.R R/features-envipick.R R/features-kpic2.R R/features-openms.R R/features-optimize-envipick.R R/features-optimize-kpic2.R R/features-optimize-openms.R R/features-optimize-xcms.R R/features-optimize-xcms3.R R/features-optimize.R R/features-safd.R R/features-set.R R/features-sirius.R R/features-tasq.R R/features-xcms.R R/features-xcms3.R R/features.R R/formulas-bruker.R R/formulas-genform.R R/formulas-set.R R/formulas-sirius.R R/formulas.R R/generics.R R/main.R R/mslibrary-json.R R/mslibrary-msp.R R/mslibrary.R R/mspeaklists-bruker.R R/mspeaklists-mzr.R R/mspeaklists-set.R R/mspeaklists.R R/multi-process-classic.R R/multi-process-future.R R/multi-process.R R/project-tool.R R/report-html-TPs.R R/report-html-components.R R/report-html-feat_annotations.R R/report-html-features.R R/report-html-utils.R R/report-html.R R/report-legacy.R R/report.R

R/sysdata.rda

R/utils-IPO.R R/utils-TPs.R R/utils-adduct.R R/utils-bruker.R R/utils-checkmate.R R/utils-components.R R/utils-compounds.R R/utils-exported.R R/utils-feat_annotations-set.R R/utils-feat_annotations.R R/utils-features.R R/utils-formulas.R R/utils-mol.R R/utils-mslibrary.R R/utils-mspeaklists.R R/utils-mzr.R R/utils-optimize.R R/utils-plot.R R/utils-progress.R R/utils-screening.R R/utils-sets.R R/utils-sirius.R R/utils-xcms.R R/utils.R R/workflow-step-set.R R/workflow-step.R R/zzz.R README.md TODO.md

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av_trigger_deps.ps1

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data-raw/adducts-genform.csv

data-raw/adducts-metfrag.csv

data-raw/compounds-scorings.csv

data-raw/prepare-data.R

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inst/CITATION

inst/REFERENCES.bib

inst/examples/optimization.R

inst/js/utils-checkUI.js

inst/js/utils-comp.js

inst/js/utils-report-legacy.js

inst/js/utils-report.js

inst/misc/IDLevelRules.yml

inst/misc/genform.txt

inst/misc/runSAFD.jl

inst/report-legacy/TPs.Rmd inst/report-legacy/annotation.Rmd inst/report-legacy/components.Rmd inst/report-legacy/featinfo.Rmd inst/report-legacy/main.Rmd inst/report/components_int.Rmd inst/report/components_nt.Rmd inst/report/components_spec.Rmd inst/report/details.Rmd inst/report/istds.Rmd

inst/report/modal.html

inst/report/report.Rmd

inst/report/settings.yml

inst/rstudio/addins.dcf

inst/templates/comp-cluster.Rmd install_patRoon.R

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man-roxygen/DA-restart-note.R man-roxygen/EICParams-arg.R man-roxygen/adduct-arg.R man-roxygen/algo_generator.R man-roxygen/algo_importer.R man-roxygen/analysisInfo-arg.R man-roxygen/as_data_table-args.R man-roxygen/centroid_note.R man-roxygen/centroid_note_mandatory.R man-roxygen/chemPropCalc.R man-roxygen/class-hierarchy.R man-roxygen/comp_algo-args.R man-roxygen/compon_algo-args.R man-roxygen/compon_gen-clust.R man-roxygen/compon_gen-feat.R man-roxygen/compon_gen-filters.R man-roxygen/compon_gen-sets-merged.R man-roxygen/components-altered-note.R man-roxygen/components_noint.R man-roxygen/consensus-common-args.R man-roxygen/consensus-form_comp.R man-roxygen/convertToMFDB.R man-roxygen/dasaveclose-args.R man-roxygen/delete.R man-roxygen/dynamictreecut.R man-roxygen/element-args.R man-roxygen/existing-generics.R man-roxygen/feat-arg.R man-roxygen/feat-filter-args.R man-roxygen/featAnnSets-class.R man-roxygen/featAnnSets-gen.R man-roxygen/featAnnSets-gen_args.R man-roxygen/filter-properties.R man-roxygen/form_algo-args.R man-roxygen/fp-args.R man-roxygen/fsubscript_source.R man-roxygen/generic-algo.R man-roxygen/generics.R man-roxygen/loadMSLibrary.R man-roxygen/loadrawdata-arg.R man-roxygen/main-rd-method.R man-roxygen/mspl_algo-args.R man-roxygen/norm-args.R man-roxygen/parallel-arg.R man-roxygen/parallelization-cache_input.R man-roxygen/plot-lim.R man-roxygen/plotChord-args.R man-roxygen/plotGraph-TPs.R man-roxygen/plotGraph.R man-roxygen/plotSpec-args.R man-roxygen/plotUpSet.R man-roxygen/plot_clust.R man-roxygen/plotsil.R man-roxygen/plotvenn-ret.R man-roxygen/pred-desc.R man-roxygen/refs-openms.R man-roxygen/rtalign-arg.R man-roxygen/sets-loadrawdata-RTalign-note.R man-roxygen/sirius-args.R man-roxygen/sirius_form-args.R man-roxygen/specSimParams-arg.R man-roxygen/spectrumType-arg.R man-roxygen/strmethod.R man-roxygen/sub_sel_del-args.R man-roxygen/tp_gen-scr.R man-roxygen/tp_gen-sim.R man-roxygen/tp_lib.R man-roxygen/tp_trans.R man-roxygen/update_comp_score-args.R man-roxygen/uses-multiProc.R man/COMStop.Rd man/EICParams.Rd man/MSLibrary-class.Rd man/MSPeakLists-class.Rd man/adduct-class.Rd man/adduct-utils.Rd man/analysis-information.Rd man/analysisinfo-dataframe.Rd man/bruker-utils.Rd man/caching.Rd man/check-GUI.Rd man/components-class.Rd man/componentsClust-class.Rd man/componentsIntClust-class.Rd man/componentsNT-class.Rd man/componentsSpecClust-class.Rd man/componentsTPs-class.Rd man/compoundScorings.Rd man/compounds-class.Rd man/compounds-cluster.Rd man/compoundsCluster-class.Rd man/compoundsMF-class.Rd man/compoundsSIRIUS-class.Rd man/convertMSFiles.Rd man/createCOMReference.Rd man/defaultOpenMSAdducts.Rd man/executeMultiProcess.Rd man/feature-filtering.Rd man/feature-optimization.Rd man/feature-plotting.Rd man/featureAnnotations-class.Rd man/featureGroups-class.Rd man/featureGroups-compare.Rd man/featureGroupsComparison-class.Rd man/featureGroupsScreening-class.Rd man/featureQualityNames.Rd man/features-class.Rd man/findFeatures.Rd man/findFeaturesBruker.Rd man/findFeaturesEnviPick.Rd man/findFeaturesKPIC2.Rd man/findFeaturesOpenMS.Rd man/findFeaturesSAFD.Rd man/findFeaturesSIRIUS.Rd man/findFeaturesXCMS.Rd man/findFeaturesXCMS3.Rd man/formulaScorings.Rd man/formulas-class.Rd man/formulasSIRIUS-class.Rd man/genFormulaTPLibrary.Rd man/generateComponents.Rd man/generateComponentsCAMERA.Rd man/generateComponentsCliqueMS.Rd man/generateComponentsIntClust.Rd man/generateComponentsNontarget.Rd man/generateComponentsOpenMS.Rd man/generateComponentsRAMClustR.Rd man/generateComponentsSpecClust.Rd man/generateComponentsTPs.Rd man/generateCompounds.Rd man/generateCompoundsLibrary.Rd man/generateCompoundsMetFrag.Rd man/generateCompoundsSIRIUS.Rd

man/generateFormulas.Rd

man/generateFormulasDA.Rd man/generateFormulasGenForm.Rd man/generateFormulasSIRIUS.Rd man/generateMSPeakLists.Rd man/generateMSPeakListsDA.Rd man/generateMSPeakListsDAFMF.Rd man/generateMSPeakListsMzR.Rd man/generateTPs.Rd man/generateTPsBioTransformer.Rd man/generateTPsCTS.Rd man/generateTPsLibrary.Rd man/generateTPsLibraryFormula.Rd man/generateTPsLogic.Rd man/generics.Rd man/getDefAvgPListParams.Rd man/getEICs.Rd man/getFCParams.Rd man/getSIRIUSToken.Rd man/groupFeatures.Rd man/groupFeaturesKPIC2.Rd man/groupFeaturesOpenMS.Rd man/groupFeaturesSIRIUS.Rd man/groupFeaturesXCMS.Rd man/groupFeaturesXCMS3.Rd man/importFeatureGroups.Rd man/importFeatureGroupsBrukerPA.Rd man/importFeatureGroupsBrukerTASQ.Rd man/importFeatureGroupsEnviMass.Rd man/importFeatureGroupsKPIC2.Rd man/importFeatureGroupsXCMS.Rd man/importFeatureGroupsXCMS3.Rd man/importFeatures.Rd man/importFeaturesEnviMass.Rd man/importFeaturesKPIC2.Rd man/importFeaturesXCMS.Rd man/importFeaturesXCMS3.Rd man/kpic2-conv.Rd man/loadMSLibrary.Rd man/loadMSLibraryMSP.Rd man/loadMSLibraryMoNAJSON.Rd

man/macros/macros.Rd

man/makeSet.Rd man/newProject.Rd man/optimizationResult-class.Rd man/patRoon-defunct.Rd man/patRoon-deprecated.Rd man/patRoon-package.Rd man/pred-aggr-params.Rd man/pred-quant.Rd man/pred-tox.Rd man/printPackageOpts.Rd man/reporting-legacy.Rd man/reporting.Rd man/sets-workflow.Rd man/specSimParams.Rd man/suspect-screening.Rd man/transformationProducts-class.Rd man/transformationProductsFormula-class.Rd man/transformationProductsStructure-class.Rd man/verifyDependencies.Rd man/withOpt.Rd man/workflowStep-class.Rd man/workflowStepSet-class.Rd man/xcms-conv.Rd

src/GenForm-svn/README

src/GenForm-svn/lgpl-2.0.txt

src/GenForm-svn/main.cpp

src/GenForm-svn/msaddion.cpp

src/GenForm-svn/msaddion.h

src/GenForm-svn/mschemelement.cpp

src/GenForm-svn/mschemelement.h

src/GenForm-svn/mscomparelr.cpp

src/GenForm-svn/mscomparelr.h

src/GenForm-svn/msconvert.cpp

src/GenForm-svn/msconvert.h

src/GenForm-svn/msdef.h

src/GenForm-svn/mselementinfo.h

src/GenForm-svn/mselementintervalmap.cpp

src/GenForm-svn/mselementintervalmap.h

src/GenForm-svn/mselementintervalmaputil.cpp

src/GenForm-svn/mselementintervalmaputil.h

src/GenForm-svn/mselementmultmap.cpp

src/GenForm-svn/mselementmultmap.h

src/GenForm-svn/mselementmultmapfilter.cpp

src/GenForm-svn/mselementmultmapfilter.h

src/GenForm-svn/mselementmultmaputil.cpp

src/GenForm-svn/mselementmultmaputil.h

src/GenForm-svn/msexception.h

src/GenForm-svn/msgenericinterval.h

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tests/testthat/test_data_sets/fg-comp-cons.Rds

tests/testthat/test_data_sets/fg-comp-kpic2.Rds

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tests/testthat/test_data_sets/fg-openms-qual.Rds

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tests/testthat/test_data_sets/fg-opt-kpic2.Rds

tests/testthat/test_data_sets/fg-opt-oms-show.txt

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tests/testthat/test_data_sets/fg-opt.Rds

tests/testthat/test_data_sets/fg-show-kpic2.txt

tests/testthat/test_data_sets/fg-show-openms-qual.txt

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tests/testthat/test_data_sets/fg-show-sirius.txt

tests/testthat/test_data_sets/fg-show-xcms.txt

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tests/testthat/test_data_sets/fg-sirius.Rds

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tests/testthat/test_data_sets/fg-xcms_import_sirius.Rds

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tests/testthat/test_data_sets/fgf-bl.txt

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tests/testthat/test_data_sets/fgf-reprsd.txt

tests/testthat/test_data_sets/formulas-DA.Rds

tests/testthat/test_data_sets/formulas-DA.txt

tests/testthat/test_data_sets/formulas-cons.Rds

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tests/testthat/test_data_sets/formulas-gf.Rds

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tests/testthat/test_data_sets/formulas-sir-fps.Rds

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tests/testthat/test_data_sets/formulas-sir.Rds

tests/testthat/test_data_sets/formulas-sir.txt

tests/testthat/test_data_sets/mslibrary-json.Rds

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tests/testthat/test_data_sets/test-mf-db-isomers.csv

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tests/testthat/test_data_sets/tp-logic.txt

vignettes/.gitignore

vignettes/_output.yml

vignettes/handbook/TPs.Rmd

vignettes/handbook/_bookdown.yml

vignettes/handbook/_output.yml

vignettes/handbook/advanced.Rmd

vignettes/handbook/bundle.png

vignettes/handbook/concepts.Rmd vignettes/handbook/generate.R vignettes/handbook/get_rdeps.R vignettes/handbook/index.Rmd vignettes/handbook/installation.Rmd vignettes/handbook/intro.Rmd vignettes/handbook/processing.Rmd vignettes/handbook/references.Rmd

vignettes/handbook/refs.bib

vignettes/handbook/sets-workflows.Rmd vignettes/handbook/setup.Rmd

vignettes/handbook/styles.css

vignettes/handbook/workflow_gen.Rmd

vignettes/newp.png

vignettes/script-post.R vignettes/script-pre.R vignettes/shared/_refs.Rmd vignettes/shared/init.R

vignettes/styles.css

vignettes/tutorial.Rmd

rickhelmus/patRoon documentation built on Sept. 17, 2024, 4:32 p.m.