Man pages for chasemc/IDBac_App
Protein and small molecule analysis of bacteria by MALDI-TOF MS

addAttribsTitle
addClassTitle
addDotsActionUIaddDotsActionUI
app_serverMain UI of IDBac
app_uiMain UI of IDBac
as.binary.matrix.hclustas.binary.matrix.hclust
availableSampleNamesSearch an IDBac database to see which sample IDs have protein...
baserMirrorPlotCreate mirror plot in base R
bootlabelsPrint bootstrap values.
bootstrapBootstrap
brukerDataSpotsandPathsUsing an excel spreadsheet, get the filepath for msconvert...
brukerToMzml_popupbrukerToMzml_popup
bsCollapseTitle
bsCollapsePanelTitle
changeDendPartColorchangeDendPartColor
changeDendPartSizechangeDendPartSize
chartoRawtoCompressedTake character, turn to raw, then compress (note:...
choose_dirChoose Directory, choose.dir vs tcltk
chooserInputchooserInput
cleanWSpacePeople have trouble with spaces
collapseReplicatesCollapse a sample's MALDIquant peak objects into a single...
colorBlindPalettecolorBlindPalette
colordendLabelsUIModify (color/size) dendrogram Labels
colordendLinesUIcolordendLinesUI
colored_dotscolored_dots I submitted this and it was pulled into...
colorPickercolorPicker for dend and dots
compresscompress Settings for compressing raw vectors
convertDataTab_ServerconvertDataTab_Server
convertDataTab_UIconvertDataTab_UI
convertDelim_ServerconvertDelim_Server
convertDelim_UIbeginWithTXT
convertMicrotyper_ServerconvertDelim_Server
convertMicrotyper_UIbeginWithTXT
convertMZ_ServerconvertMZ_Server
convertMZ_UIbeginWithMZ
convertOneBruker_ServerconvertOneBruker_Server
convertOneBruker_UIoneMaldiPlate
copyDB_dbAttachAttach new database to existing database
copyDB_setupMetaSetup metadata DB table
copyingDbPopupWhile Database is copying, block user-interaction
copyToNewDatabaseCopy from one database to another, selecting by Sample ID
createMetaSQLcreateMetaSQL
createNewSQLITEdbCreate New, Empty SQLite Database
createPoolCreate a pool connecton, given file names and a path If there...
createSpectraSQLcreateSpectraSQL
createXMLSQLcreateXMLSQL
databaseSelector_serverdatabaseSelector_server
databaseSelector_UIdatabaseSelector_UI
databaseTabServerdatabaseTabServer
databaseTabUILayout for the databaseTabUI
databaseTabUIFuncdatabaseTabUIFunc
decompressdecompress Settings for decompressing in IDBac, serialized...
dendDotsServerTitle
dendDotsUIModify (color/size) dendrogram lines
dendrogramCreatordendrogramCreator
dendrogramCreatorUIdendrogramCreatorUI
deserialdeserial Settings for serializing in IDBac (convert to json)
displayMissingProteinUIDisplay samples removed from analysis
distMatrixCreate Distance Matrix
dot-calculateMatches.calculateMatches
dot-clust.clust
dot-grepAcquDoubleValue.grepAcquDoubleValue
dot-grepAcquValue.grepAcquValue
dot-resampleresample
dot-sampleName.sampleName
dot-text.coord.hclust.text.coord.hclust
downloadHierDownload newick hierarchical dendrogram
downloadSmNet_UIdownloadSmNet_UI
downloadSvgDownload svg hierarchical dendrogram
dropNullsfrom shinyBS
experimentSummary_ServerexperimentSummary_Server
experimentSummary_UIexperimentSummary_UI
exportmzMLExport mzML/mzXML from SQLite DB
exportSamples_serverexportSamples_server
exportSamples_uiExport samples from database
extractHPCConstantsfrom https://github.com/sgibb/readBrukerFlexData
findAcquisitionInfofindAcquisitionInfo
findMSconvertTitle
findmzFind mzML and mzXML files
findRawSHAandFilefindRawSHAandFile
getAllStrain_IDsfromSQLgetAllStrain_IDsfromSQL
getAttribsTitle
getOSGet OS
getPeakDataRetrieve MALDIquant peak objects from an IDBac sqlite...
getSmallMolSpectraRetrieve small molecule and matrix peak lists and make...
hashRhashR Settings for hashing in IDBac
insertIntoIndividualSpectraWrite individual spectra to SQLite
insertIntoMassTableWrite massTable data to SQLite
insertMetadataColumnsInsert columns into IDBac SQLite metadata table
labelsFromBrushedDendrogramnetworkViaBrushedDendrogram
manPageProtDend_ServermanPageProtDend_Server
manPageProtDend_UImanPageProtDend_UI
MAN_ServerMAN_Server
microtyperTomzMLParse Microtyper files
mirrorPlotCreate mirror plot
mirrorPlotDownload_UImirrorPlotDownload_UI
mirrorPlots_ServerTitle
mirrorPlotsSettings_UImirrorPlotsSettings_UI
mirrorPlots_UImirrorPlots_UI
modDendDotsMod_WellPanelmodDendDotsMod_WellPanel UI
modDendLabels_WellPanelmodDendLabels_WellPanel UI
modDendLines_WellPanelmodDendLines_WellPanel UI
mquantSpecFromSQLmquantSpecFromSQL
mQuantToMassVecMALDIquant to Mass Vectors
multipleMaldiPlatesmultipleMaldiPlates
parseDelimitedMSparseDelimitedMS
path_sanitizeSanitize a filename by removing directory paths and invalid...
pcaCalculationPrinciple Components Analysis Given a data frame whose...
pcoaCalculationPrinciple Coordinates Analysis Given a data frame whose...
peakBinnerpeakBinner
peakRetentionSettings_ServerpeakRetentionSettings_Server
peakRetentionSettings_UIpeakRetentionSettings_UI
plateMapUIplateMapUI
platemodplatemod
plotHierplotHier
plotly_3d_scatterCreate 3d scatter plotly plot
popup3popup3
popup4popup4
popupPlot_serverpopupPlot_server
popupPlotTsne_serverpopupPlot_server
popupPlotTsne_UIUI module for creating absolute panel popup
popupPlot_UIUI module for creating absolute panel popup
processMZMLprocessMZML
processProteinSpectraprocessProteinSpectra
processSmallMolSpectraprocessSmallMolSpectra
processXMLIndSpectraProcess spectra data for input into SQLite
proteinPeaksToMatrixproteinPeaksToMatrix
readAcquFileTitle
run_apprun_app
runDendDotsRun Dend and dots
sampleChooser_serverServer for choosing all samples fromm an IDBac DB
sampleChooser_UIUI for choosing all samples fromm an IDBac DB
sampMetasampMeta
sampMetaOutputsampMetaOutput
selectDirectory_ServerselectDirectory_Server
selectDirectory_UIselectDirectory_UI
selectInjections_serverInject samples from another database into dendrogram
selectInjections_UIselectInjections_UI
serialserial Settings for serializing in IDBac (convert to json)
serializeXMLRead mzXML, XML and transform to raw character for storing in...
smallmirrorPlotsSampleSelect_UImirrorPlotsSettings_UI
smallmirrorPlots_ServerTitle
smallmirrorPlots_UIsmallmirrorPlots_UI
smallMolDendrogram_UIsmallMolDendrogram_UI
smallMolDFtoNetworkCollapse a sample's MALDIquant peak objects into a single...
smMANPlot_UIsmMANPlot_UI
spectraProcessingFunctionCreate IDBac SQLite database Should work for mzML, mzXML,...
spectrumMatrixToMALDIqauntSQL to MALDIquant
sql_CreateIndividualSpectraSQL code to create the SQLite IndividualSpectra table
sql_CreatemassTableSQL code to create the SQLite massTable table
sql_CreatemetaDataSQL code to create the SQLite metaData table
sqlCreate_versionCreate version table
sql_CreateVersionTableSQL code to create the SQLite version table
sql_CreatexmlTableSQL code to create the SQLite xml table
sqlTableArchitecturesqlTableArchitecture
startingFromBrukerFlexWhen user is starting with Bruker Flex file(s)
startingFromMZWhen user is starting with mzML/mzXML file(s)
subtractMatrixBlankSubtract "matrix" sample masses from sample peak lists
transferToNewDB_servertransferToNewDB_server
transferToNewDB_UItransferToNewDB
tsneCalculationt-SNE Analysis Given a data frame whose columns are variables...
tsneUiPoptSNE UI
ui_proteinClusteringui_proteinClustering
ui_smallMolManui_smallMolMan
updateCollapsefrom shinyBS
updateMeta_serverupdateMeta_server
updateMeta_UIupdateMeta_UI
chasemc/IDBac_App documentation built on March 25, 2019, 6:58 p.m.