addAttribs | Title |
addClass | Title |
addDotsActionUI | addDotsActionUI |
app_server | Main UI of defb |
app_ui | Main UI of defb |
as.binary.matrix.hclust | as.binary.matrix.hclust |
availableSampleNames | Search an defb database to see which sample IDs have protein... |
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 |
cleanWSpace | People have trouble with spaces |
collapseReplicates | Collapse a sample's MALDIquant peak objects into a single... |
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 |
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_setupMeta | Setup metadata DB table |
copyingDbPopup | While Database is copying, block user-interaction |
copyToNewDatabase | Copy from one database to another, selecting by Sample ID |
createMetaSQL | createMetaSQL |
createNewSQLITEdb | Create New, Empty SQLite Database |
createPool | Create a pool connecton, given file names and a path If there... |
createSpectraSQL | createSpectraSQL |
createXMLSQL | createXMLSQL |
databaseSelector_server | databaseSelector_server |
databaseSelector_UI | databaseSelector_UI |
databaseTabServer | databaseTabServer |
databaseTabUI | Layout for the databaseTabUI |
databaseTabUIFunc | databaseTabUIFunc |
decompress | decompress Settings for decompressing in defb, serialized... |
dendDotsServer | Title |
dendDotsUI | Modify (color/size) dendrogram lines |
dendrogramCreator | dendrogramCreator |
dendrogramCreatorUI | dendrogramCreatorUI |
deserial | deserial Settings for serializing in defb (convert to json) |
displayMissingProteinUI | Display samples removed from analysis |
distMatrix | Create Distance Matrix |
dot-calculateMatches | .calculateMatches |
dot-clust | .clust |
dot-grepAcquDoubleValue | .grepAcquDoubleValue |
dot-grepAcquValue | .grepAcquValue |
dot-resample | resample |
dot-sampleName | .sampleName |
dot-text.coord.hclust | .text.coord.hclust |
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 |
extractHPCConstants | from https://github.com/sgibb/readBrukerFlexData |
findMissingSampleMapIds | Find which MALDI-target spots have data but an ID wasn't... |
findMSconvert | Title |
findmz | Find mzML and mzXML files |
getAllStrain_IDsfromSQL | getAllStrain_IDsfromSQL |
getAttribs | Title |
getOS | Get OS |
getPeakData | Retrieve MALDIquant peak objects from an defb sqlite database |
getSmallMolSpectra | Retrieve small molecule and matrix peak lists and make... |
hashR | hashR Settings for hashing in defb |
insertIntoIndividualSpectra | Write individual spectra to SQLite |
insertIntoMassTable | Write massTable data to SQLite |
insertLocale | Insert current locale info into sql table |
insertMetadataColumns | Insert columns into defb SQLite metadata table |
labelsFromBrushedDendrogram | networkViaBrushedDendrogram |
manPageProtDend_Server | manPageProtDend_Server |
manPageProtDend_UI | manPageProtDend_UI |
MAN_Server | MAN_Server |
map384Well | Create 384-well matrix map |
microtyperTomzML | Parse Microtyper files |
mirrorPlot | Create mirror plot |
mirrorPlotDownload_UI | mirrorPlotDownload_UI |
mirrorPlots_Server | Title |
mirrorPlotsSettings_UI | mirrorPlotsSettings_UI |
mirrorPlots_UI | mirrorPlots_UI |
modDendDotsMod_WellPanel | modDendDotsMod_WellPanel UI |
modDendLabels_WellPanel | modDendLabels_WellPanel UI |
modDendLines_WellPanel | modDendLines_WellPanel UI |
modularityClustering | Color network based on fastgreedy.community |
mquantSpecFromSQL | mquantSpecFromSQL |
mQuantToMassVec | #' Bin MALDI peaks #' #' @param peakList list of MALDIquant... |
multipleMaldiPlates | multipleMaldiPlates |
networkFromDF | Network from data frame |
nulledMap384Well | Create a 384-well matrix that is NA-filled |
parseDelimitedMS | parseDelimitedMS |
path_sanitize | Sanitize a filename by removing directory paths and invalid... |
pcaCalculation | Principle Components Analysis Given a data frame whose... |
pcoaCalculation | Principle Coordinates Analysis Given a data frame whose... |
peakBinner | Peak List Binner |
peakRetentionSettings_Server | peakRetentionSettings_Server |
peakRetentionSettings_UI | peakRetentionSettings_UI |
plateMapUI | plateMapUI |
platemod | platemod |
plotHier | plotHier |
plotly_3d_scatter | Create 3d scatter plotly plot |
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 |
processMZML | processMZML |
processProteinSpectra | processProteinSpectra |
processSmallMolSpectra | processSmallMolSpectra |
processXMLIndSpectra | Process spectra data for input into SQLite |
proteinPeaksToMatrix | proteinPeaksToMatrix |
proteoWizConvert | When user is starting with Bruker Flex file(s) |
readAcqusFile | Read Bruker Acqus File |
readBrukerAcqus | findBrukerTargetSpots |
run_app | run_app |
runDendDots | Run Dend and dots |
sampleChooser_server | Server for choosing all samples fromm an defb DB |
sampleChooser_UI | UI for choosing all samples fromm an defb DB |
sampleMapSaver | Update sample map reactive value |
sampleMapViewer | Editable Sample Map |
sampMeta | sampMeta |
sampMetaOutput | sampMetaOutput |
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 defb (convert to json) |
serializeXML | Read mzXML, XML and transform to raw character for storing in... |
smallmirrorPlotsSampleSelect_UI | mirrorPlotsSettings_UI |
smallmirrorPlots_Server | Title |
smallmirrorPlots_UI | smallmirrorPlots_UI |
smallMolDendrogram_UI | smallMolDendrogram_UI |
smallMolDFtoNetwork | Collapse a sample's MALDIquant peak objects into a single... |
smMANPlot_UI | smMANPlot_UI |
spectraProcessingFunction | Create defb SQLite database Should work for mzML, mzXML, mgf,... |
spectrumMatrixToMALDIqaunt | SQL to MALDIquant |
sql_CreateIndividualSpectra | SQL code to create the SQLite IndividualSpectra table |
sql_CreatelLocaleTable | SQL code to create the SQLite locale table |
sql_CreatemassTable | SQL code to create the SQLite massTable table |
sql_CreatemetaData | SQL code to create the SQLite metaData table |
sqlCreate_version | Create version table |
sql_CreateVersionTable | SQL code to create the SQLite version table |
sql_CreatexmlTable | SQL code to create the SQLite xml table |
sqlTableArchitecture | sqlTableArchitecture |
startingFromMZ | When user is starting with mzML/mzXML file(s) |
subtractMatrixBlank | Subtract "matrix" sample masses from sample peak lists |
transferToNewDB_server | transferToNewDB_server |
transferToNewDB_UI | transferToNewDB |
tsneCalculation | t-SNE Analysis Given a data frame whose columns are variables... |
tsneUiPop | tSNE UI |
ui_proteinClustering | ui_proteinClustering |
ui_smallMolMan | ui_smallMolMan |
updateCollapse | from shinyBS |
updateMeta_server | updateMeta_server |
updateMeta_UI | updateMeta_UI |
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