| addAttribs | Title |
| addClass | Title |
| appendDendLabsUI | Append metadata to the dendrogrm's labels |
| app_server | Main UI of IDBac |
| app_ui | Main UI of IDBac |
| as.binary.matrix.hclust | as.binary.matrix.hclust |
| assembleMirrorPlots | Assemble mirror plot Data |
| baserMirrorPlot | Create mirror plot in base R |
| bootlabels | Print bootstrap values. |
| bootstrap | Bootstrap |
| brukerToMzml_popup | brukerToMzml_popup |
| bsCollapse | Title |
| bsCollapsePanel | Title |
| changeDendPartColor | changeDendPartColor |
| changeDendPartSize | changeDendPartSize |
| chartoRawtoCompressed | Take character, turn to raw, then compress |
| choose_dir | Choose Directory, choose.dir vs tcltk |
| chooserInput | chooserInput |
| colorBlindPalette | colorBlindPalette |
| colordendLabelsUI | Modify (color/size) dendrogram Labels |
| colordendLinesUI | colordendLinesUI |
| colored_dots | colored_dots I submitted this and it was pulled into... |
| colorMANBy_UI | Color MAN settings |
| colorPicker | colorPicker for dend and dots |
| compress | compress Settings for compressing raw vectors |
| controlBrukerDisplay | Controls display of Bruker conversion page |
| convertDataTab_Server | convertDataTab_Server |
| convertDataTab_UI | convertDataTab_UI |
| convertDelim_Server | convertDelim_Server |
| convertDelim_UI | beginWithTXT |
| convertMicrotyper_Server | convertDelim_Server |
| convertMicrotyper_UI | beginWithTXT |
| convertMZ_Server | convertMZ_Server |
| convertMZ_UI | beginWithMZ |
| convertOneBruker_Server | convertOneBruker_Server |
| convertOneBruker_UI | oneMaldiPlate |
| copyDB_dbAttach | Attach new database to existing database |
| copyDB_dbDetach | Detach new database to existing database |
| copyDB_setupMeta | Setup metadata DB table |
| copyingDbPopup | While Database is copying, block user-interaction |
| copyToNewDatabase | Copy from one database to another, selecting by Sample ID |
| createFuzzyVector | High-dimensional representation of mass peaks |
| createFuzzyVectorUnit | Experimental binning |
| createMetaSQL | createMetaSQL |
| createNewSQLITEdb | Create New, Empty SQLite Database |
| createSpectraSQL | createSpectraSQL |
| createXMLSQL | createXMLSQL |
| current_db_version | Single point of reference for latest db version |
| databaseSelector_server | databaseSelector_server |
| databaseSelector_UI | databaseSelector_UI |
| databaseTabServer | databaseTabServer |
| databaseTabUI | Layout for the databaseTabUI |
| databaseTabUIFunc | databaseTabUIFunc |
| db_from_bruker | Convert Bruker raw fids to IDBac database |
| db_from_mzml | db_from_mzml |
| decompress | decompress Settings for decompressing in IDBac, serialized... |
| delim_to_mzml | Parse Delimited MS files with fread and MALDIquant |
| dendDotsServer | Title |
| dendDotsUI | Modify (color/size) dendrogram lines |
| dendrogramActionsUI | dendrogramActionsUI |
| dendrogramCreator | Title |
| dendrogramCreatorUI | dendrogramCreatorUI |
| deserial | deserial spectrum json (single json array) Settings for... |
| displayMissingProteinUI | Display samples removed from analysis |
| distMatrix | Create Distance Matrix |
| dot-calculateMatches | .calculateMatches |
| dot-checkPool | Check if a pool object |
| dot-clust | .clust |
| dot-copy_db | Copy an IDBac database, appending db version number |
| dot-db_path_from_pool | Find database path from pool object |
| dot-download_idbac_exe | Download IDBac exe |
| dot-getLatestStableVersionPage | GET api.github.com page for latest release |
| dot-get_one_subtree | Recursively look for a tree within a tree |
| dot-getSmallPeaksFromBrush | Retrieve small molecule and matrix peak lists and make... |
| dot-grepAcquDoubleValue | .grepAcquDoubleValue |
| dot-grepAcquValue | .grepAcquValue |
| dot-parse_json_peaks | Create maldiquant peaks from IDBac SQL peak JSON |
| dot-resample | resample |
| dot-retrieve_peaks_from_pool | Retrieve MALDIquant peak objects from an IDBac sqlite... |
| dot-sampleName | .sampleName |
| dot-scale_ppm | scaler so smallest mass differnce is 1 |
| dot-text.coord.hclust | .text.coord.hclust |
| double_from_raw_compressed | Convert raw compresed data from sqlite into R vector |
| downloadHier | Download newick hierarchical dendrogram |
| downloadSmNet_UI | downloadSmNet_UI |
| downloadSvg | Download svg hierarchical dendrogram |
| dropNulls | from shinyBS |
| experimentSummary_Server | experimentSummary_Server |
| experimentSummary_UI | experimentSummary_UI |
| exportmzML | Export mzML/mzXML from SQLite DB |
| exportSamples_server | exportSamples_server |
| exportSamples_ui | Export samples from database |
| extractBrukerAcquistionInfo | Find a certain Bruker Acqus info |
| extractHPCConstants | from https://github.com/sgibb/readBrukerFlexData |
| findIdbacHome | Get default path for IDBac to save experiments to |
| findMissingSampleMapIds | Find which MALDI-target spots have data but an ID wasn't... |
| findMSconvert | Find proteowizard's msconvert.exe |
| find_mz_files | Find mzML and mzXML files |
| getAttribs | Title |
| getMicrotyperFiles | getMicrotyperFiles |
| getOS | Get OS |
| get_subtrees | Get subtree |
| hashR | hashR Settings for hashing in IDBac |
| idbac_available_samples | Search an IDBac database to see which sample IDs have protein... |
| idbac_connect | Create a pool connecton, given file names and a path If there... |
| idbac_create | Title |
| idbac_db_version | Get the IDBac version that created the database |
| idbac_dendrogram_creator | dendrogramCreator |
| idbac_get_metadata | Extract a metadata column |
| idbac_get_peaks | Collapse a sample's MALDIquant peak objects into a single... |
| idbac_get_spectra | Get spectra from database |
| idbac_update_db | Update IDBac Database from version 1 to 2 |
| insertIntoIndividualSpectra | Write individual spectra to SQLite |
| insertIntoMassTable | Write mass_index data to SQLite |
| insertMetadataColumns | Insert columns into IDBac SQLite metadata table |
| labelsFromBrushedDendrogram | networkViaBrushedDendrogram |
| manPageProtDend_Server | manPageProtDend_Server |
| manPageProtDend_UI | manPageProtDend_UI |
| MAN_Server | MAN_Server |
| map384Well | Create 384-well matrix map |
| merge_idbac_experiments | Merge all samples from IDBac sqlite databses |
| microtyperTomzML | readMicrotyperFiles |
| mirrorPlot | Create mirror plot |
| mirrorPlotDownload_UI | mirrorPlotDownload_UI |
| mirrorPlots_Server | Title |
| mirrorPlotsSettings_UI | mirrorPlotsSettings_UI |
| mirrorPlots_UI | mirrorPlots_UI |
| modAppendDendLabels_WellPanel | modAppendDendLabels_WellPanel UI |
| modDendDotsMod_WellPanel | modDendDotsMod_WellPanel UI |
| modDendLabels_WellPanel | modDendLabels_WellPanel UI |
| modDendLines_WellPanel | modDendLines_WellPanel UI |
| modularityClustering | Color network based on fastgreedy.community |
| mquant_bin | MALDIquant binning |
| multipleMaldiPlates | multipleMaldiPlates |
| networkFromDF | Network from data frame |
| newUpdate | News/Update module |
| new_version_check | Check if there's a new stable version of IDBac |
| normalizeSpectrumIntensity | Smooth, remove baseline, and normalize intensity of a... |
| nulledMap384Well | Create a 384-well matrix that is NA-filled |
| pcaCalculation | Principle Components Analysis |
| pcoaCalculation | Principle Coordinates Analysis |
| peakRetentionSettings_Server | peakRetentionSettings_Server |
| peakRetentionSettings_UI | peakRetentionSettings_UI |
| pipe | Pipe operator |
| plateMapUI | plateMapUI |
| platemod | platemod |
| plotDendrogram | Function for plotting dendrogram |
| plotHier | plotHier |
| plotly_3d_scatter | Create 3d scatter plotly plot |
| poolToCon | Checkout pool if it isn't |
| popup3 | popup3 |
| popup4 | popup4 |
| popupPlot_server | popupPlot_server |
| popupPlotTsne_server | popupPlot_server |
| popupPlotTsne_UI | UI module for creating absolute panel popup |
| popupPlot_UI | UI module for creating absolute panel popup |
| prioritizer | Prioritize Samples |
| processProteinSpectra | Process protein spectra with MALDIquant |
| processSmallMolSpectra | Process small molecule spectra with MALDIquant |
| processXMLIndSpectra | Process spectra data for input into SQLite |
| proteinPeaksToMatrix | proteinPeaksToMatrix |
| proteoWizConvert | Convert raw data with msconvert |
| readAcqusFile | Read Bruker Acqus File |
| readBrukerAcqus | findBrukerTargetSpots |
| retrieveAllStrainIds | retrieveAllStrainIds |
| run_app | run_app |
| runDendDots | Run Dend and dots |
| run_microtyperTomzML | run_microtyperTomzML setup and loop |
| sampleChooser_server | Server for choosing all samples fromm an IDBac DB |
| sampleChooser_UI | UI for choosing all samples fromm an IDBac DB |
| sampleMaptoDF | Update sample map reactive value |
| sampleMapViewer | Rhandsontable Sample Map |
| sanitize | Sanitize a filename by removing directory paths and invalid... |
| saveNetSVG | Title |
| selectDirectory_Server | selectDirectory_Server |
| selectDirectory_UI | selectDirectory_UI |
| selectInjections_server | Inject samples from another database into dendrogram |
| selectInjections_UI | selectInjections_UI |
| serial | serial Settings for serializing in IDBac (convert to json) |
| serializeXML | Read mzXML, xml and transform to raw character for storing in... |
| small_maldiquant_to_network | Collapse a sample's MALDIquant peak objects into a single... |
| smallmirrorPlotsSampleSelect_UI | mirrorPlotsSettings_UI |
| smallmirrorPlots_Server | Title |
| smallmirrorPlots_UI | smallmirrorPlots_UI |
| smallMolDendrogram_UI | smallMolDendrogram_UI |
| smMANPlot_UI | smMANPlot_UI |
| spectraProcessingFunction | Create IDBac SQLite database Should work for mzML, mzXML,... |
| spectrumMatrixToMALDIqaunt | SQL to MALDIquant |
| sql_create_locale_table | SQL code to create the SQLite locale table |
| sql_create_massindex_table | SQL code to create the SQLite mass_index table |
| sql_create_metadata_table | SQL code to create the SQLite metadata table |
| sql_create_spectra_table | SQL code to create the SQLite spectra table |
| sql_create_version_table | SQL code to create the SQLite version table |
| sql_create_xml_table | SQL code to create the SQLite xml table |
| sql_fill_locale_table | Insert current locale info into sql table |
| sql_fill_version_table | Create version table |
| subtractMatrixBlank | Subtract "matrix" sample masses from sample peak lists |
| transferToNewDB_server | transferToNewDB_server |
| transferToNewDB_UI | transferToNewDB |
| tsneCalculation | t-SNE Analysis |
| tsneUiPop | tSNE UI |
| ui_proteinClustering | ui_proteinClustering |
| ui_smallMolMan | ui_smallMolMan |
| updateCollapse | from shinyBS |
| update_idbac_modal | Display update info |
| updateMeta_server | updateMeta_server |
| updateMeta_UI | updateMeta_UI |
