Files in mjhelf/Mosaic
Metaboseek platform
.Rbuildignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/ISSUE_TEMPLATE/help.md
.github/ISSUE_TEMPLATE/other-issues.md
.github/workflows/linux-build.yml
.github/workflows/macOS-build.yml
.github/workflows/windows-build.yml
.gitignore
.travis.yml
DESCRIPTION
LICENSE
Mosaic.Rproj
NAMESPACE
R/Classes.R
R/Container_FeatureTableContainer.R
R/Container_FilterContainer.R
R/Container_MainPageContainer.R
R/Container_MainPlotContainer.R
R/Container_MseekContainer.R
R/Container_OptionsContainer.R
R/Documentation_templates.R
R/Function_MseekOptions.R
R/Function_PlotWindow.R
R/Function_massquery.R
R/Function_runMseek.R
R/Function_specplot.R
R/Functions_FeatureTable_analysis.R
R/Functions_Labelfinder.R
R/Functions_SIRIUS.R
R/Functions_calcMZ.R
R/Functions_class_MSdata.R
R/Functions_class_featureTable.R
R/Functions_deprecated.R
R/Functions_extract_EICs.R
R/Functions_extract_Scans.R
R/Functions_featureReport.R
R/Functions_formatting_utilities.R
R/Functions_graph_utilities.R
R/Functions_math_utilities.R
R/Functions_peakPicking.R
R/Functions_plotting_EICs.R
R/Functions_plotting_genericData.R
R/Functions_rcdk.R
R/Functions_retcorAdjust.R
R/Functions_xcmsRunner.R
R/Module_ChangeFTGroupingModule.R
R/Module_EICOptionsModule.R
R/Module_EICmodule.R
R/Module_FeatureReportModule.R
R/Module_FilePathModule.R
R/Module_FilterModule.R
R/Module_FindMS2scansModule.R
R/Module_FindPatternsModule.R
R/Module_GetIntensitiesModule.R
R/Module_GlobalOptionsModule.R
R/Module_GroupedEICModule.R
R/Module_LabelFinderModule.R
R/Module_LoadDataModule.R
R/Module_LoadMSDataModule.R
R/Module_LoadNetworkModule.R
R/Module_LoadSessionModule.R
R/Module_LoadTableModule.R
R/Module_MS2BrowserModule.R
R/Module_MZcalcModule.R
R/Module_MainTableModule.R
R/Module_MassShiftsModule.R
R/Module_MatchReferenceModule.R
R/Module_MultiEICmodule.R
R/Module_MultiFilterModule.R
R/Module_MultiSpecmodule.R
R/Module_MzqueryModule.R
R/Module_NetworkModule.R
R/Module_PcaViewModule.R
R/Module_PeakPickModule.R
R/Module_PeptideAnnotationModule.R
R/Module_PeptideCalcModule.R
R/Module_PeptideModificationsModule.R
R/Module_PlotBrowserModule.R
R/Module_PlotModule.R
R/Module_QuickPlotModule.R
R/Module_RatioPlotModule.R
R/Module_RegroupMSDataModule.R
R/Module_RenameTableModule.R
R/Module_RtCorrViewModule.R
R/Module_SaveNetworkModule.R
R/Module_SaveSessionModule.R
R/Module_SaveTableModule.R
R/Module_SelectActiveTableModule.R
R/Module_SelectMS2Module.R
R/Module_SelectMSGroupingModule.R
R/Module_SelectProjectFolderModule.R
R/Module_ShowSiriusModule.R
R/Module_SimplifyNetworkModule.R
R/Module_SiriusModule.R
R/Module_SiriusOptionsModule.R
R/Module_SpecModule2.R
R/Module_Specmodule.R
R/Module_TableAnalysisModule.R
R/Module_TableModule.R
R/Module_UploadTableModule.R
R/Module_VennDiagramModule.R
R/Module_WelcomePageModule.R
R/Module_columnSelModule.R
R/Module_updaterModule.R
R/Server_components.R
R/UI_components.R
R/Widget_DownloadPlotWidget.R
R/Widget_GetSiriusWidget.R
R/Widget_ModalWidget.R
R/Widget_MseekHistoryWidget.R
R/Widget_PeptideSequencePlotWidget.R
R/Widget_SpecModuleWidget.R
R/Widget_SwitchButton.R
R/Widget_TableModule2.R
R/Widget_VennWidgetModule.R
R/Widget_densPlotWidget.R
R/Widget_simpleTableModule.R
R/Widget_xcmsWidget.R
R/getset_MSData.R
R/getset_featureTables.R
R/methods_MseekFamily.R
R/methods_MseekGraph.R
R/methods_Spectrum.R
R/methods_analyzeFT.R
R/methods_buildMseekFT.R
R/zzz.R
README.md
appveyor.yml
inst/Metaboseek/global.R
inst/Metaboseek/server.R
inst/Metaboseek/ui.R
inst/Metaboseek/www/img/mosaic_logo.png
inst/NEWS.html
inst/PeptideApp/app.R
inst/app/global.R
inst/app/server.R
inst/app/ui.R
inst/app/www/img/mosaic_logo.png
inst/config/Metaboseek_styles.css
inst/config/variableMods.tsv
inst/config/xcms/Metaboseek_defaults/camera.csv
inst/config/xcms/Metaboseek_defaults/centWave.csv
inst/config/xcms/Metaboseek_defaults/description.txt
inst/config/xcms/Metaboseek_defaults/group.csv
inst/config/xcms/Metaboseek_defaults/outputs.csv
inst/config/xcms/Metaboseek_defaults/peakfilling.csv
inst/config/xcms/Metaboseek_defaults/retcor.csv
inst/config/xcms/xcms_defaults/camera.csv
inst/config/xcms/xcms_defaults/centWave.csv
inst/config/xcms/xcms_defaults/description.txt
inst/config/xcms/xcms_defaults/group.csv
inst/config/xcms/xcms_defaults/outputs.csv
inst/config/xcms/xcms_defaults/peakfilling.csv
inst/config/xcms/xcms_defaults/retcor.csv
inst/db/HMDB_detected.csv
inst/db/HMDB_detected_neg.csv
inst/db/HMDB_detected_pos.csv
inst/db/LipidBLAST_mz_trimmed_neg.csv
inst/db/LipidBLAST_mz_trimmed_pos.csv
inst/db/smid-db.csv
inst/db/smid-db_neg.csv
inst/db/smid-db_pos.csv
inst/examples/MseekContainer.R
inst/extdata/examples/example_projectfolder/AnalysisSessionInfo.txt
inst/extdata/examples/example_projectfolder/RTcorr_data.Rds
inst/extdata/examples/example_projectfolder/analysis_groups.csv
inst/extdata/examples/example_projectfolder/camera.csv
inst/extdata/examples/example_projectfolder/centWave.csv
inst/extdata/examples/example_projectfolder/filegroups_base.csv
inst/extdata/examples/example_projectfolder/group.csv
inst/extdata/examples/example_projectfolder/large_example_features.csv
inst/extdata/examples/example_projectfolder/mini_example_features.csv
inst/extdata/examples/example_projectfolder/outputs.csv
inst/extdata/examples/example_projectfolder/peakfilling.csv
inst/extdata/examples/example_projectfolder/peaktable_grouped_RTcorr_filled.mskFT
inst/extdata/examples/example_projectfolder/postProcessingSettings.json
inst/extdata/examples/example_projectfolder/settings.zip
inst/extdata/examples/example_projectfolder/status.csv
inst/extdata/examples/example_projectfolder/xcms_runner_i.R
inst/extdata/examples/ms1/mut/AA03.mzXML
inst/extdata/examples/ms1/mut/AA05.mzXML
inst/extdata/examples/ms1/mut/AA07.mzXML
inst/extdata/examples/ms1/wt/AA10.mzXML
inst/extdata/examples/ms1/wt/AA12.mzXML
inst/extdata/examples/ms1/wt/AA14.mzXML
inst/extdata/examples/ms1/wt/AA16.mzXML
inst/extdata/examples/ms2/mut/AA01.mzXML
inst/extdata/examples/ms2/wt/AA04.mzXML
inst/extdata/examples/networking_data/GNPS_Networking_example.zip
inst/extdata/examples/peptide_demo/LLI_peptide.csv
inst/scripts/install_Metaboseek.R
inst/scripts/update_script.R
inst/scripts/xcms_runner_i.R
man/ChangeFTGroupingModule.Rd
man/ColumnSelModule.Rd
man/DownloadPlotWidget.Rd
man/EICOptionsModule.Rd
man/EICgeneral.Rd
man/EICmodule.Rd
man/EICplot.Rd
man/EICtitles.Rd
man/FTAnalysisParam-class.Rd
man/FTAnalysisParam.Rd
man/FTProcessHistory-class.Rd
man/FTProcessHistory.Rd
man/FTselection.Rd
man/FeatureReportModule.Rd
man/FeatureTable.Rd
man/FeatureTableContainer.Rd
man/FilePathModule.Rd
man/FilterContainer.Rd
man/FilterModule.Rd
man/FindMS2ScansModule.Rd
man/FindPatternsModule.Rd
man/FunParam-class.Rd
man/FunParam.Rd
man/GetIntensitiesModule.Rd
man/GetSiriusWidget.Rd
man/GlobalOptionsModule.Rd
man/GroupedEICModule.Rd
man/LabelFinderModule.Rd
man/ListToReactiveValues.Rd
man/LoadDataModule.Rd
man/LoadMSDataModule.Rd
man/LoadNetworkModule.Rd
man/LoadSessionModule.Rd
man/LoadTableModule.Rd
man/MS2BrowserModule.Rd
man/MZcalcModule.Rd
man/MainPageContainer.Rd
man/MainPlotContainer.Rd
man/MainTableModule.Rd
man/MassShiftsModule.Rd
man/MatchReferenceModule.Rd
man/ModalWidget.Rd
man/MosCluster.Rd
man/Mseek.colors.Rd
man/MseekAnova.Rd
man/MseekContainer.Rd
man/MseekContainers.Rd
man/MseekExamplePreload.Rd
man/MseekFamily.Rd
man/MseekGraphs.Rd
man/MseekHistoryWidget.Rd
man/MseekMinimalServer.Rd
man/MseekMinimalUI.Rd
man/MseekModules.Rd
man/MseekOptions.Rd
man/MseekWidgets.Rd
man/MultiEICmodule.Rd
man/MultiFilterModule.Rd
man/MultiSpecModule.Rd
man/MzqueryModule.Rd
man/NetworkModule.Rd
man/OptionsContainer.Rd
man/Parentsearch.Rd
man/PcaViewModule.Rd
man/PeakPickModule.Rd
man/PeptideAnnotationModule.Rd
man/PeptideCalcModule.Rd
man/PeptideModificationsModule.Rd
man/PeptideSequencePlotWidget.Rd
man/PlotBrowserModule.Rd
man/PlotModule.Rd
man/PlotWindow.Rd
man/QuickPlotsModule.Rd
man/RTplot.Rd
man/RatioPlotModule.Rd
man/RegroupMSDataModule.Rd
man/RenameTableModule.Rd
man/RtCorrViewModule.Rd
man/SaveNetworkModule.Rd
man/SaveSessionModule.Rd
man/SaveTableModule.Rd
man/SelectActiveTableModule.Rd
man/SelectMS2Module.Rd
man/SelectMSGroupingModule.Rd
man/SelectProjectFolderModule.Rd
man/ShowSiriusModule.Rd
man/SimplifyNetworkModule.Rd
man/SiriusModule.Rd
man/SiriusOptionsModule.Rd
man/SpecModule2.Rd
man/Specmodule.Rd
man/SpecplotWidget.Rd
man/SwitchButton.Rd
man/TableAnalysisModule.Rd
man/TableModule.Rd
man/TableModule2.Rd
man/TableUpdateChunk.Rd
man/UploadTableModule.Rd
man/VennDiagramModule.Rd
man/VennWidgetModule.Rd
man/WelcomePageModule.Rd
man/activeFT.Rd
man/addLines.Rd
man/analyzeFT.Rd
man/analyzeTable.Rd
man/asInclusionlist.Rd
man/asMetaboAnalyst.Rd
man/assignColor.Rd
man/bestgauss.Rd
man/buildMseekFT.Rd
man/calcMZs.Rd
man/cameraWrapper.Rd
man/checkFolders.Rd
man/colorRampLegend.Rd
man/constructFeatureTable.Rd
man/constructRawLayout.Rd
man/dashboardHeaderM.Rd
man/densPlotWidget.Rd
man/densplot.Rd
man/dot-calculateM.Rd
man/dot-getFTFormat.Rd
man/dot-reformatFeatureTable.Rd
man/dot-withHistory.Rd
man/exIntensities.Rd
man/fastPeakShapes.Rd
man/featlistCompare.Rd
man/featureCalcs.Rd
man/featureReport.Rd
man/featureTableNormalize.Rd
man/filenamemaker.Rd
man/findLabeledPeaks.Rd
man/findLabels.Rd
man/findMSnScans.Rd
man/find_peaks2.Rd
man/findsubgraph.Rd
man/foldChange.Rd
man/getAllScans.Rd
man/getFilters.Rd
man/getScanInfo.Rd
man/getSirius.Rd
man/getSiriusTree.Rd
man/getSpectra.Rd
man/get_common_dir.Rd
man/getgauss.Rd
man/getpeaks2.Rd
man/gm_mean.Rd
man/groupPlot.Rd
man/groupedplot.Rd
man/layout_components_qgraph.Rd
man/legendplot.Rd
man/listMS2scans.Rd
man/loadMseekSession.Rd
man/loadRawM.Rd
man/mActionButton.Rd
man/mDownloadButton.Rd
man/makeColorscheme.Rd
man/makeRTlist2.Rd
man/makeScanlist2.Rd
man/massquery.Rd
man/matchedToCharacter.Rd
man/mergeMSold.Rd
man/mergecollectlist.Rd
man/mergepeaks2.Rd
man/multiEIC.Rd
man/multiEICplus.Rd
man/multittest.Rd
man/mzMatch.Rd
man/parsePatterns.Rd
man/parseTitle.Rd
man/peakDetect.Rd
man/peakFitter.Rd
man/peakFunction.Rd
man/plotSMILE.Rd
man/plotTree.Rd
man/plotlyTextFormatter.Rd
man/plotpeaks.Rd
man/quickMergeMS.Rd
man/rawEICm.Rd
man/rawGrouping.Rd
man/reactiveValuesToListRec.Rd
man/reconstructValues.Rd
man/reverselog_trans.Rd
man/rtadjust.Rd
man/rtexport.Rd
man/runMseek.Rd
man/runSirius.Rd
man/safelog.Rd
man/saveMseekSession.Rd
man/saveScanlist.Rd
man/savetable.Rd
man/simpleTableModule.Rd
man/simplifyGraph.Rd
man/specplot.Rd
man/specplot2.Rd
man/subsetEICs.Rd
man/tableGrouping.Rd
man/tableWriter.Rd
man/updateDF.Rd
man/updateFT.Rd
man/updateFTIndex.Rd
man/updateFTgrouping.Rd
man/updateFeatureTable.Rd
man/updateRawLayout.Rd
man/updaterModule.Rd
man/values.Rd
man/writeMS.Rd
man/writeStatus.Rd
man/xcmsWidget.Rd
mosaic.Rproj
tests/testthat.R
tests/testthat/FullMseek/app.R
tests/testthat/FullMseek/expected_testresult.json
tests/testthat/FullMseek/expected_testresult_build.json
tests/testthat/FullMseek/tests/mytest-expected/001.json
tests/testthat/FullMseek/tests/mytest-expected/001.png
tests/testthat/FullMseek/tests/mytest.R
tests/testthat/FullMseek/www/img/mosaic_logo.png
tests/testthat/test_EICs.R
tests/testthat/test_app.R
tests/testthat/test_class_feature_table.R
tests/testthat/test_class_msdata.R
tests/testthat/test_colorranges.R
tests/testthat/test_feature_table_data_analysis.R
tests/testthat/test_methods_MseekFT.R
tests/testthat/test_xcmsRunner.R
vignettes/.gitignore
vignettes/Getting_Started.Rmd
vignettes/METABOseek_for_developers.Rmd
vignettes/assets/columnLegend.csv
vignettes/bibliography.bib
vignettes/img/Analysis_SearchMS2.png
vignettes/img/Analyze_Table.png
vignettes/img/Data_Explorer_overview.png
vignettes/img/FTA_Analyze_Table.png
vignettes/img/FTA_Filter_Table.png
vignettes/img/FTA_Regroup_Table.png
vignettes/img/Feature_Table.png
vignettes/img/Feature_Table_History.png
vignettes/img/Feature_Table_Save_Table.png
vignettes/img/General_Browse.gif
vignettes/img/MS2browser_FeatureReport.gif
vignettes/img/MS2browser_FinishNetwork.png
vignettes/img/MS2browser_ScanList.png
vignettes/img/MS2browser_Sirius_results.png
vignettes/img/MS2browser_Sirius_start.png
vignettes/img/MS2browser_makeEdges.png
vignettes/img/MS2browser_network_match-to-ref.png
vignettes/img/MS2browser_networking.gif
vignettes/img/MS2browser_overview.png
vignettes/img/MS2browser_simplifyNetwork.png
vignettes/img/Mseek_Navbar_screenshot.png
vignettes/img/Options_EIC_options.png
vignettes/img/Options_Mass_shifts.png
vignettes/img/Options_Molecular_Formulas.png
vignettes/img/Options_RT_corr.png
vignettes/img/Options_SIRIUS.png
vignettes/img/SIRIUS.gif
vignettes/img/Screenshot_866x650.png
vignettes/img/browse_2.gif
vignettes/img/logo_web_full.png
vignettes/img/logo_web_full_240.png
vignettes/img/networking.gif
vignettes/img/outputFiles.png
vignettes/img/startPage.png
vignettes/img/xcmsAnalysis.png
vignettes/style.css
