├── .Rbuildignore ├── .gitattributes ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── IDBac_App.Rproj ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── 0_current_database_version.R ├── app_run_app.R ├── app_server.R ├── app_ui.R ├── fct_assembleMirrorPlots.R ├── fct_availableSampleNames.R ├── fct_bootstrap.R ├── fct_chooseDirectory.R ├── fct_colored_Dots.R ├── fct_convertBruker.R ├── fct_delete_samples.R ├── fct_dendrogramCreator.R ├── fct_dendrogramModifiers.R ├── fct_distanceMatrix.R ├── fct_extractBrukerAcqInfo.R ├── fct_findIdbacHomeFolder.R ├── fct_findMSconvert.R ├── fct_findMissingSampleMapIds.R ├── fct_getSmallPeaksFromBrush.R ├── fct_getSubTrees.R ├── fct_idbacRetrievePeaksFromPool.R ├── fct_idbac_double_from_raw_compressed.R ├── fct_idbac_getSpectra.R ├── fct_idbac_get_peaks.R ├── fct_labelsFromBrushedDendrogram.R ├── fct_mergeDb.R ├── fct_metadataFromId.R ├── fct_mirrorPlots.R ├── fct_multidimensionalAnalyses.R ├── fct_networkFromDF.R ├── fct_normalizeSpectrumIntensity.R ├── fct_parseDelimitedMS.R ├── fct_parseMicrotyper.R ├── fct_pathSanitize.R ├── fct_peakFuzzifier.R ├── fct_plotly_3d_scatter.R ├── fct_prioritizer.R ├── fct_processMZML.R ├── fct_processXMLIndSpectra.R ├── fct_proteinPeaksToMatrix.r ├── fct_proteoWizConvert.R ├── fct_readBrukerAcqus.R ├── fct_readBrukerAcqusFile.r ├── fct_runDendDots.R ├── fct_smallMolDFtoNetwork.R ├── fct_spectraProcessingFunction.r ├── fct_spectraToPeaks.R ├── fct_subtractMatrixBlank.R ├── fct_updateIdbac.R ├── module_MANS.R ├── module_ModifyDendrogramLabels.R ├── module_ModifyDendrogramLines.R ├── module_appendToDendrogramLabels.R ├── module_convertBruker.R ├── module_convertDelim.R ├── module_convertMZ.R ├── module_convertMicrotyper.R ├── module_data_conversion.R ├── module_databaseSelector.R ├── module_databaseTab.R ├── module_dendInject.R ├── module_dend_and_dots.R ├── module_dendrogram.R ├── module_dendrogramCreator.R ├── module_directorySelect.R ├── module_experimentSummary.R ├── module_export.R ├── module_mirrorPlots.R ├── module_news.R ├── module_plateMap.R ├── module_plotDendrogram.R ├── module_popupPlots.R ├── module_proteinPeaksToRetainSelections.R ├── module_sampleChooser.R ├── module_smallMirror.R ├── module_transferToNewDB.R ├── module_tsne.R ├── module_upddateMets.R ├── onLoad.R ├── searchNCBI.R ├── sql_connect.R ├── sql_copyToNewDatabase.r ├── sql_create_database.R ├── sql_dbCreators.R ├── sql_db_version.R ├── sql_exportmzML.R ├── sql_getDatabaseVersion.R ├── sql_insertMetadataColumns.R ├── sql_retrieveAllStrainIds.r ├── sql_spectrumMatrixToMALDIqaunt.R ├── sql_sqlTableArchitecture.r ├── sql_updateDatabaseVersion.R ├── ui_MAN.R ├── ui_chooserInput.r ├── ui_colorPicker.R ├── ui_popups.R ├── ui_proteinClustering.R ├── ui_shinyBS.R ├── utils-pipe.R └── utils.R ├── README.md ├── inst ├── app │ ├── server.R │ └── ui.R ├── prioritization_report.Rmd └── www │ ├── GitHub.png │ ├── IDBac_Computer_SVG_300DPI.png │ ├── Multi-MALDI-Plate.png │ ├── Single-MALDI-Plate.png │ ├── SmallAppIcon3.ico │ ├── WorkingDirectory.png │ ├── WorkingDirectory_ReAnalysis.png │ ├── big_bacPlate.jpg │ ├── chooser-binding.js │ ├── collapse │ ├── shinyBS.css │ └── shinyBS.js │ ├── css.css │ ├── cssloader │ ├── assets │ │ ├── spinner.css │ │ └── spinner.js │ └── css-loaders │ │ ├── .gitignore │ │ ├── Gruntfile.js │ │ ├── LICENSE │ │ ├── README.md │ │ ├── bower.json │ │ ├── css │ │ ├── fallback.css │ │ ├── load1.css │ │ ├── load2.css │ │ ├── load3.css │ │ ├── load4.css │ │ ├── load5.css │ │ ├── load6.css │ │ ├── load7.css │ │ └── load8.css │ │ ├── images │ │ └── css-loaders-screenshot.jpg │ │ ├── less │ │ ├── fallback.less │ │ ├── load1.less │ │ ├── load2.less │ │ ├── load3.less │ │ ├── load4.less │ │ ├── load5.less │ │ ├── load6.less │ │ ├── load7.less │ │ └── load8.less │ │ ├── package.json │ │ └── sass │ │ ├── fallback.scss │ │ ├── load1.scss │ │ ├── load2.scss │ │ ├── load3.scss │ │ ├── load4.scss │ │ ├── load5.scss │ │ ├── load6.scss │ │ ├── load7.scss │ │ └── load8.scss │ ├── icon_svg.svg │ └── styles.css ├── man ├── MAN_Server.Rd ├── addAttribs.Rd ├── addClass.Rd ├── app_server.Rd ├── app_ui.Rd ├── appendDendLabsUI.Rd ├── as.binary.matrix.hclust.Rd ├── assembleMirrorPlots.Rd ├── baserMirrorPlot.Rd ├── bootlabels.Rd ├── bootstrap.Rd ├── brukerToMzml_popup.Rd ├── bsCollapse.Rd ├── bsCollapsePanel.Rd ├── changeDendPartColor.Rd ├── changeDendPartSize.Rd ├── chartoRawtoCompressed.Rd ├── choose_dir.Rd ├── chooserInput.Rd ├── colorBlindPalette.Rd ├── colorMANBy_UI.Rd ├── colorPicker.Rd ├── colordendLabelsUI.Rd ├── colordendLinesUI.Rd ├── colored_dots.Rd ├── compress.Rd ├── controlBrukerDisplay.Rd ├── convertDataTab_Server.Rd ├── convertDataTab_UI.Rd ├── convertDelim_Server.Rd ├── convertDelim_UI.Rd ├── convertMZ_Server.Rd ├── convertMZ_UI.Rd ├── convertMicrotyper_Server.Rd ├── convertMicrotyper_UI.Rd ├── convertOneBruker_Server.Rd ├── convertOneBruker_UI.Rd ├── copyDB_dbAttach.Rd ├── copyDB_dbDetach.Rd ├── copyDB_setupMeta.Rd ├── copyToNewDatabase.Rd ├── copyingDbPopup.Rd ├── createFuzzyVector.Rd ├── createFuzzyVectorUnit.Rd ├── createMetaSQL.Rd ├── createNewSQLITEdb.Rd ├── createSpectraSQL.Rd ├── createXMLSQL.Rd ├── current_db_version.Rd ├── databaseSelector_UI.Rd ├── databaseSelector_server.Rd ├── databaseTabServer.Rd ├── databaseTabUI.Rd ├── databaseTabUIFunc.Rd ├── db_from_bruker.Rd ├── db_from_mzml.Rd ├── decompress.Rd ├── delim_to_mzml.Rd ├── dendDotsServer.Rd ├── dendDotsUI.Rd ├── dendrogramActionsUI.Rd ├── dendrogramCreator.Rd ├── dendrogramCreatorUI.Rd ├── deserial.Rd ├── displayMissingProteinUI.Rd ├── distMatrix.Rd ├── dot-calculateMatches.Rd ├── dot-checkPool.Rd ├── dot-clust.Rd ├── dot-copy_db.Rd ├── dot-db_path_from_pool.Rd ├── dot-download_idbac_exe.Rd ├── dot-getLatestStableVersionPage.Rd ├── dot-getSmallPeaksFromBrush.Rd ├── dot-get_one_subtree.Rd ├── dot-grepAcquDoubleValue.Rd ├── dot-grepAcquValue.Rd ├── dot-parse_json_peaks.Rd ├── dot-resample.Rd ├── dot-retrieve_peaks_from_pool.Rd ├── dot-sampleName.Rd ├── dot-scale_ppm.Rd ├── dot-text.coord.hclust.Rd ├── double_from_raw_compressed.Rd ├── downloadHier.Rd ├── downloadSmNet_UI.Rd ├── downloadSvg.Rd ├── dropNulls.Rd ├── experimentSummary_Server.Rd ├── experimentSummary_UI.Rd ├── exportSamples_server.Rd ├── exportSamples_ui.Rd ├── exportmzML.Rd ├── extractBrukerAcquistionInfo.Rd ├── extractHPCConstants.Rd ├── findIdbacHome.Rd ├── findMSconvert.Rd ├── findMissingSampleMapIds.Rd ├── find_mz_files.Rd ├── getAttribs.Rd ├── getMicrotyperFiles.Rd ├── getOS.Rd ├── get_subtrees.Rd ├── hashR.Rd ├── idbac_available_samples.Rd ├── idbac_connect.Rd ├── idbac_create.Rd ├── idbac_db_version.Rd ├── idbac_dendrogram_creator.Rd ├── idbac_get_metadata.Rd ├── idbac_get_peaks.Rd ├── idbac_get_spectra.Rd ├── idbac_update_db.Rd ├── insertIntoIndividualSpectra.Rd ├── insertIntoMassTable.Rd ├── insertMetadataColumns.Rd ├── labelsFromBrushedDendrogram.Rd ├── manPageProtDend_Server.Rd ├── manPageProtDend_UI.Rd ├── map384Well.Rd ├── merge_idbac_experiments.Rd ├── microtyperTomzML.Rd ├── mirrorPlot.Rd ├── mirrorPlotDownload_UI.Rd ├── mirrorPlotsSettings_UI.Rd ├── mirrorPlots_Server.Rd ├── mirrorPlots_UI.Rd ├── modAppendDendLabels_WellPanel.Rd ├── modDendDotsMod_WellPanel.Rd ├── modDendLabels_WellPanel.Rd ├── modDendLines_WellPanel.Rd ├── modularityClustering.Rd ├── mquant_bin.Rd ├── multipleMaldiPlates.Rd ├── networkFromDF.Rd ├── newUpdate.Rd ├── new_version_check.Rd ├── normalizeSpectrumIntensity.Rd ├── nulledMap384Well.Rd ├── pcaCalculation.Rd ├── pcoaCalculation.Rd ├── peakRetentionSettings_Server.Rd ├── peakRetentionSettings_UI.Rd ├── pipe.Rd ├── plateMapUI.Rd ├── platemod.Rd ├── plotDendrogram.Rd ├── plotHier.Rd ├── plotly_3d_scatter.Rd ├── poolToCon.Rd ├── popup3.Rd ├── popup4.Rd ├── popupPlotTsne_UI.Rd ├── popupPlotTsne_server.Rd ├── popupPlot_UI.Rd ├── popupPlot_server.Rd ├── prioritizer.Rd ├── processProteinSpectra.Rd ├── processSmallMolSpectra.Rd ├── processXMLIndSpectra.Rd ├── proteinPeaksToMatrix.Rd ├── proteoWizConvert.Rd ├── readAcqusFile.Rd ├── readBrukerAcqus.Rd ├── retrieveAllStrainIds.Rd ├── runDendDots.Rd ├── run_app.Rd ├── run_microtyperTomzML.Rd ├── sampleChooser_UI.Rd ├── sampleChooser_server.Rd ├── sampleMapViewer.Rd ├── sampleMaptoDF.Rd ├── sanitize.Rd ├── saveNetSVG.Rd ├── selectDirectory_Server.Rd ├── selectDirectory_UI.Rd ├── selectInjections_UI.Rd ├── selectInjections_server.Rd ├── serial.Rd ├── serializeXML.Rd ├── smMANPlot_UI.Rd ├── smallMolDendrogram_UI.Rd ├── small_maldiquant_to_network.Rd ├── smallmirrorPlotsSampleSelect_UI.Rd ├── smallmirrorPlots_Server.Rd ├── smallmirrorPlots_UI.Rd ├── spectraProcessingFunction.Rd ├── spectrumMatrixToMALDIqaunt.Rd ├── sql_create_locale_table.Rd ├── sql_create_massindex_table.Rd ├── sql_create_metadata_table.Rd ├── sql_create_spectra_table.Rd ├── sql_create_version_table.Rd ├── sql_create_xml_table.Rd ├── sql_fill_locale_table.Rd ├── sql_fill_version_table.Rd ├── subtractMatrixBlank.Rd ├── transferToNewDB_UI.Rd ├── transferToNewDB_server.Rd ├── tsneCalculation.Rd ├── tsneUiPop.Rd ├── ui_proteinClustering.Rd ├── ui_smallMolMan.Rd ├── updateCollapse.Rd ├── updateMeta_UI.Rd ├── updateMeta_server.Rd └── update_idbac_modal.Rd └── tests ├── testthat.R └── testthat ├── Rplots.pdf ├── test-.R ├── test-00_create_database.R ├── test-01_create_database.R ├── test-02_createfuzzyvector.R ├── test-bootstrap.R ├── test-brukerToMzml_popup.R ├── test-colored_dots.R ├── test-colorpalette.R ├── test-controlBrukerDisplay.R ├── test-copyDB_setupMeta.R ├── test-copy_db.R ├── test-databasetransfer.R ├── test-db_path_from_pool.R ├── test-db_update.R ├── test-dbcreators.R ├── test-distMatrix.R ├── test-findIdbacHome.R ├── test-findMSconvert.R ├── test-findmissingsamplemapids.R ├── test-getMicrotyperFiles.R ├── test-getPeakData.R ├── test-hashr.R ├── test-insertlocale.R ├── test-labelsfrombrusheddendrogram.R ├── test-map384well.R ├── test-mirrorplots.R ├── test-module_databasetab.R ├── test-module_dendrogram.R ├── test-module_tsne.R ├── 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