Man pages for chasemc/IDBacApp
MALDI-TOF MS Protien and Small Molecule Analysis

addAttribsTitle
addClassTitle
appendDendLabsUIAppend metadata to the dendrogrm's labels
app_serverMain UI of IDBac
app_uiMain UI of IDBac
as.binary.matrix.hclustas.binary.matrix.hclust
assembleMirrorPlotsAssemble mirror plot Data
baserMirrorPlotCreate mirror plot in base R
bootlabelsPrint bootstrap values.
bootstrapBootstrap
brukerToMzml_popupbrukerToMzml_popup
bsCollapseTitle
bsCollapsePanelTitle
changeDendPartColorchangeDendPartColor
changeDendPartSizechangeDendPartSize
chartoRawtoCompressedTake character, turn to raw, then compress
choose_dirChoose Directory, choose.dir vs tcltk
chooserInputchooserInput
colorBlindPalettecolorBlindPalette
colordendLabelsUIModify (color/size) dendrogram Labels
colordendLinesUIcolordendLinesUI
colored_dotscolored_dots I submitted this and it was pulled into...
colorMANBy_UIColor MAN settings
colorPickercolorPicker for dend and dots
compresscompress Settings for compressing raw vectors
controlBrukerDisplayControls display of Bruker conversion page
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_dbDetachDetach 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
createFuzzyVectorHigh-dimensional representation of mass peaks
createFuzzyVectorUnitExperimental binning
createMetaSQLcreateMetaSQL
createNewSQLITEdbCreate New, Empty SQLite Database
createSpectraSQLcreateSpectraSQL
createXMLSQLcreateXMLSQL
current_db_versionSingle point of reference for latest db version
databaseSelector_serverdatabaseSelector_server
databaseSelector_UIdatabaseSelector_UI
databaseTabServerdatabaseTabServer
databaseTabUILayout for the databaseTabUI
databaseTabUIFuncdatabaseTabUIFunc
db_from_brukerConvert Bruker raw fids to IDBac database
db_from_mzmldb_from_mzml
decompressdecompress Settings for decompressing in IDBac, serialized...
delim_to_mzmlParse Delimited MS files with fread and MALDIquant
dendDotsServerTitle
dendDotsUIModify (color/size) dendrogram lines
dendrogramActionsUIdendrogramActionsUI
dendrogramCreatorTitle
dendrogramCreatorUIdendrogramCreatorUI
deserialdeserial spectrum json (single json array) Settings for...
displayMissingProteinUIDisplay samples removed from analysis
distMatrixCreate Distance Matrix
dot-calculateMatches.calculateMatches
dot-checkPoolCheck if a pool object
dot-clust.clust
dot-copy_dbCopy an IDBac database, appending db version number
dot-db_path_from_poolFind database path from pool object
dot-download_idbac_exeDownload IDBac exe
dot-getLatestStableVersionPageGET api.github.com page for latest release
dot-get_one_subtreeRecursively look for a tree within a tree
dot-getSmallPeaksFromBrushRetrieve small molecule and matrix peak lists and make...
dot-grepAcquDoubleValue.grepAcquDoubleValue
dot-grepAcquValue.grepAcquValue
dot-parse_json_peaksCreate maldiquant peaks from IDBac SQL peak JSON
dot-resampleresample
dot-retrieve_peaks_from_poolRetrieve MALDIquant peak objects from an IDBac sqlite...
dot-sampleName.sampleName
dot-scale_ppmscaler so smallest mass differnce is 1
dot-text.coord.hclust.text.coord.hclust
double_from_raw_compressedConvert raw compresed data from sqlite into R vector
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
extractBrukerAcquistionInfoFind a certain Bruker Acqus info
extractHPCConstantsfrom https://github.com/sgibb/readBrukerFlexData
findIdbacHomeGet default path for IDBac to save experiments to
findMissingSampleMapIdsFind which MALDI-target spots have data but an ID wasn't...
findMSconvertFind proteowizard's msconvert.exe
find_mz_filesFind mzML and mzXML files
getAttribsTitle
getMicrotyperFilesgetMicrotyperFiles
getOSGet OS
get_subtreesGet subtree
hashRhashR Settings for hashing in IDBac
idbac_available_samplesSearch an IDBac database to see which sample IDs have protein...
idbac_connectCreate a pool connecton, given file names and a path If there...
idbac_createTitle
idbac_db_versionGet the IDBac version that created the database
idbac_dendrogram_creatordendrogramCreator
idbac_get_metadataExtract a metadata column
idbac_get_peaksCollapse a sample's MALDIquant peak objects into a single...
idbac_get_spectraGet spectra from database
idbac_update_dbUpdate IDBac Database from version 1 to 2
insertIntoIndividualSpectraWrite individual spectra to SQLite
insertIntoMassTableWrite mass_index data to SQLite
insertMetadataColumnsInsert columns into IDBac SQLite metadata table
labelsFromBrushedDendrogramnetworkViaBrushedDendrogram
manPageProtDend_ServermanPageProtDend_Server
manPageProtDend_UImanPageProtDend_UI
MAN_ServerMAN_Server
map384WellCreate 384-well matrix map
merge_idbac_experimentsMerge all samples from IDBac sqlite databses
microtyperTomzMLreadMicrotyperFiles
mirrorPlotCreate mirror plot
mirrorPlotDownload_UImirrorPlotDownload_UI
mirrorPlots_ServerTitle
mirrorPlotsSettings_UImirrorPlotsSettings_UI
mirrorPlots_UImirrorPlots_UI
modAppendDendLabels_WellPanelmodAppendDendLabels_WellPanel UI
modDendDotsMod_WellPanelmodDendDotsMod_WellPanel UI
modDendLabels_WellPanelmodDendLabels_WellPanel UI
modDendLines_WellPanelmodDendLines_WellPanel UI
modularityClusteringColor network based on fastgreedy.community
mquant_binMALDIquant binning
multipleMaldiPlatesmultipleMaldiPlates
networkFromDFNetwork from data frame
newUpdateNews/Update module
new_version_checkCheck if there's a new stable version of IDBac
normalizeSpectrumIntensitySmooth, remove baseline, and normalize intensity of a...
nulledMap384WellCreate a 384-well matrix that is NA-filled
pcaCalculationPrinciple Components Analysis
pcoaCalculationPrinciple Coordinates Analysis
peakRetentionSettings_ServerpeakRetentionSettings_Server
peakRetentionSettings_UIpeakRetentionSettings_UI
pipePipe operator
plateMapUIplateMapUI
platemodplatemod
plotDendrogramFunction for plotting dendrogram
plotHierplotHier
plotly_3d_scatterCreate 3d scatter plotly plot
poolToConCheckout pool if it isn't
popup3popup3
popup4popup4
popupPlot_serverpopupPlot_server
popupPlotTsne_serverpopupPlot_server
popupPlotTsne_UIUI module for creating absolute panel popup
popupPlot_UIUI module for creating absolute panel popup
prioritizerPrioritize Samples
processProteinSpectraProcess protein spectra with MALDIquant
processSmallMolSpectraProcess small molecule spectra with MALDIquant
processXMLIndSpectraProcess spectra data for input into SQLite
proteinPeaksToMatrixproteinPeaksToMatrix
proteoWizConvertConvert raw data with msconvert
readAcqusFileRead Bruker Acqus File
readBrukerAcqusfindBrukerTargetSpots
retrieveAllStrainIdsretrieveAllStrainIds
run_apprun_app
runDendDotsRun Dend and dots
run_microtyperTomzMLrun_microtyperTomzML setup and loop
sampleChooser_serverServer for choosing all samples fromm an IDBac DB
sampleChooser_UIUI for choosing all samples fromm an IDBac DB
sampleMaptoDFUpdate sample map reactive value
sampleMapViewerRhandsontable Sample Map
sanitizeSanitize a filename by removing directory paths and invalid...
saveNetSVGTitle
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...
small_maldiquant_to_networkCollapse a sample's MALDIquant peak objects into a single...
smallmirrorPlotsSampleSelect_UImirrorPlotsSettings_UI
smallmirrorPlots_ServerTitle
smallmirrorPlots_UIsmallmirrorPlots_UI
smallMolDendrogram_UIsmallMolDendrogram_UI
smMANPlot_UIsmMANPlot_UI
spectraProcessingFunctionCreate IDBac SQLite database Should work for mzML, mzXML,...
spectrumMatrixToMALDIqauntSQL to MALDIquant
sql_create_locale_tableSQL code to create the SQLite locale table
sql_create_massindex_tableSQL code to create the SQLite mass_index table
sql_create_metadata_tableSQL code to create the SQLite metadata table
sql_create_spectra_tableSQL code to create the SQLite spectra table
sql_create_version_tableSQL code to create the SQLite version table
sql_create_xml_tableSQL code to create the SQLite xml table
sql_fill_locale_tableInsert current locale info into sql table
sql_fill_version_tableCreate version table
subtractMatrixBlankSubtract "matrix" sample masses from sample peak lists
transferToNewDB_servertransferToNewDB_server
transferToNewDB_UItransferToNewDB
tsneCalculationt-SNE Analysis
tsneUiPoptSNE UI
ui_proteinClusteringui_proteinClustering
ui_smallMolManui_smallMolMan
updateCollapsefrom shinyBS
update_idbac_modalDisplay update info
updateMeta_serverupdateMeta_server
updateMeta_UIupdateMeta_UI
chasemc/IDBacApp documentation built on Oct. 22, 2022, 2:52 a.m.