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
.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_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_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_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_RegroupMSDataModule.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_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_Spectrum.R R/methods_analyzeFT.R R/methods_buildMseekFT.R R/zzz.R README.md
appveyor.yml
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/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/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/RegroupMSDataModule.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/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-withHistory.Rd man/exIntensities.Rd man/fastPeakShapes.Rd man/featureCalcs.Rd man/featureReport.Rd man/featureTableNormalize.Rd man/filenamemaker.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/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/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/img/Analyze_Table.png
vignettes/img/outputFiles.png
vignettes/img/startPage.png
vignettes/img/xcmsAnalysis.png
vignettes/style.css
mjhelf/Mosaic documentation built on Sept. 23, 2019, 5:45 a.m.