Files in chasemc/tempRepo
Protein and small molecule analysis of bacteria by MALDI-TOF MS

.Rbuildignore
.gitattributes
.gitignore
.travis.yml
DESCRIPTION
LICENSE.md
MALDI-Plate_Template/384_Spot_MALDI_Template.xltx
MALDIparameters/AutoXMethods/IDBac_Protein_AutoX.axe
MALDIparameters/AutoXMethods/IDBac_Small-Molecule_autoX.axe
MALDIparameters/flexAnalysisMethods/Protein_Calibrant-Calibration.FAMSMethod
MALDIparameters/flexAnalysisMethods/Protein_Unknown-Sample-Calibration.FAMSMethod
MALDIparameters/flexAnalysisMethods/SmallMolecule-Calibrant-Calibration.FAMSMethod
MALDIparameters/flexAnalysisMethods/SmallMolecule-Unknown-Sample-Calibration.FAMSMethod
MALDIparameters/flexControlMethods/IDBac_Protein.par
MALDIparameters/flexControlMethods/IDBac_SmallMolecule.par
NAMESPACE
R/addStrainAttributesModal.r R/app_server.r R/app_ui.R R/availableSampleNames.R R/binnR.r R/bootstrap.R R/chooseDir.r R/chooserInput.r R/collapseReplicates.R R/colored_Dots.r R/copyToNewDatabase.r R/createPool.R R/dbCreators.R R/dendrogramModifiers.r R/distanceMatrix.r R/hierMetaInputModule.R R/labelsFromBrushedDendrogram.R R/manipulateMetadata.R R/mirrorPlot_functions.R R/module_MANS.R R/module_convertBruker.R R/module_convertDelim.R R/module_convertMZ.R R/module_convertMicrotyper.R R/module_data_conversion.R R/module_databaseSelector.R R/module_databaseTab.R R/module_dendInject.R R/module_dendrogram.R R/module_dendrogramCreator.R R/module_directorySelect.R R/module_experimentSummary.R R/module_export.R R/module_mirrorPlots.R R/module_plateMap.R R/module_popupPlots.R R/module_proteinPeaksToRetainSelections.R R/module_sampleChooser.R R/module_smallMirror.R R/module_transferToNewDB.R R/module_tsne.R R/module_upddateMets.R R/multidimensionalAnalysis.R R/mzXML_machineData_readHelpers.r R/onLoad.R R/parseDelimitedMS.R R/parseMicrotyper.R R/pathSanitize.R
R/peakBinner.R
R/plotly_3d_scatter.R R/popups.R R/processMZML.R R/processXMLIndSpectra.R R/proteinPeaksToMatrix.r R/rawDataHandlers.R R/readBrukerAcqusFile.r R/run_app.R R/savemzfromSQL.R R/searchNCBI.R R/shinyBS.R R/smallMolDFtoNetwork.R R/smallMoleculeSpectraFunctions.R R/spectraProcessingFunction.r R/spectraToPeaks.R R/sqlManipulators.r R/sqlTableArchitecture.r R/sqlToMaldiquant.R R/subtractMatrixBlank.R R/test_examples.R R/ui_MAN.R R/ui_proteinClustering.R R/utils.R README.md
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appveyor.yml
inst/app/server.r inst/app/ui.r
inst/extdata/RawData/0_C1/1/1SLin/acqu
inst/extdata/RawData/0_C1/1/1SLin/acqus
inst/extdata/RawData/0_C1/1/1SLin/fid
inst/extdata/RawData/0_C1/1/1SLin/pdata/1/1r
inst/extdata/RawData/0_C1/1/1SLin/pdata/1/proc
inst/extdata/RawData/0_C1/1/1SLin/pdata/1/procs
inst/extdata/RawData/0_C1/1/1SLin/sptype
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inst/extdata/icon/browserconfig.xml
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inst/extdata/icon/icon.ico
inst/extdata/icon/mstile-150x150.png
inst/extdata/icon/safari-pinned-tab.svg
inst/extdata/icon/site.webmanifest
inst/extdata/mzml/mzml.mzML
inst/extdata/sqlite/sample.sqlite
inst/www/A.png
inst/www/GitHub.png
inst/www/IDBacLogo.png
inst/www/IDBac_Computer_SVG_300DPI.png
inst/www/Multi-MALDI-Plate.png
inst/www/PCA.gif
inst/www/Single-MALDI-Plate.png
inst/www/SmallAppIcon3.ico
inst/www/WorkingDirectory.png
inst/www/WorkingDirectory_ReAnalysis.png
inst/www/arrowRight.png
inst/www/big_bacPlate.jpg
inst/www/chooser-binding.js
inst/www/collapse/shinyBS.css
inst/www/collapse/shinyBS.js
inst/www/css.css
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inst/www/cssloader/assets/spinner.js
inst/www/cssloader/css-loaders/.gitignore
inst/www/cssloader/css-loaders/Gruntfile.js
inst/www/cssloader/css-loaders/LICENSE
inst/www/cssloader/css-loaders/README.md
inst/www/cssloader/css-loaders/bower.json
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man/MAN_Server.Rd man/addAttribs.Rd man/addClass.Rd man/addDotsActionUI.Rd man/app_server.Rd man/app_ui.Rd man/as.binary.matrix.hclust.Rd man/availableSampleNames.Rd man/baserMirrorPlot.Rd man/bootlabels.Rd man/bootstrap.Rd man/brukerDataSpotsandPaths.Rd man/brukerToMzml_popup.Rd man/bsCollapse.Rd man/bsCollapsePanel.Rd man/changeDendPartColor.Rd man/changeDendPartSize.Rd man/chartoRawtoCompressed.Rd man/choose_dir.Rd man/chooserInput.Rd man/cleanWSpace.Rd man/collapseReplicates.Rd man/colorBlindPalette.Rd man/colorPicker.Rd man/colordendLabelsUI.Rd man/colordendLinesUI.Rd man/colored_dots.Rd man/compress.Rd man/convertDataTab_Server.Rd man/convertDataTab_UI.Rd man/convertDelim_Server.Rd man/convertDelim_UI.Rd man/convertMZ_Server.Rd man/convertMZ_UI.Rd man/convertMicrotyper_Server.Rd man/convertMicrotyper_UI.Rd man/convertOneBruker_Server.Rd man/convertOneBruker_UI.Rd man/copyDB_dbAttach.Rd man/copyDB_setupMeta.Rd man/copyToNewDatabase.Rd man/copyingDbPopup.Rd man/createMetaSQL.Rd man/createNewSQLITEdb.Rd man/createPool.Rd man/createSpectraSQL.Rd man/createXMLSQL.Rd man/databaseSelector_UI.Rd man/databaseSelector_server.Rd man/databaseTabServer.Rd man/databaseTabUI.Rd man/databaseTabUIFunc.Rd man/decompress.Rd man/dendDotsServer.Rd man/dendDotsUI.Rd man/dendrogramCreator.Rd man/dendrogramCreatorUI.Rd man/deserial.Rd man/displayMissingProteinUI.Rd man/distMatrix.Rd man/dot-calculateMatches.Rd man/dot-clust.Rd man/dot-grepAcquDoubleValue.Rd man/dot-grepAcquValue.Rd man/dot-resample.Rd man/dot-sampleName.Rd man/dot-text.coord.hclust.Rd man/downloadHier.Rd man/downloadSmNet_UI.Rd man/downloadSvg.Rd man/dropNulls.Rd man/experimentSummary_Server.Rd man/experimentSummary_UI.Rd man/exportSamples_server.Rd man/exportSamples_ui.Rd man/exportmzML.Rd man/extractHPCConstants.Rd man/findAcquisitionInfo.Rd man/findMSconvert.Rd man/findRawSHAandFile.Rd man/findmz.Rd man/getAllStrain_IDsfromSQL.Rd man/getAttribs.Rd man/getOS.Rd man/getPeakData.Rd man/getSmallMolSpectra.Rd man/hashR.Rd man/insertIntoIndividualSpectra.Rd man/insertIntoMassTable.Rd man/insertMetadataColumns.Rd man/labelsFromBrushedDendrogram.Rd man/mQuantToMassVec.Rd man/manPageProtDend_Server.Rd man/manPageProtDend_UI.Rd man/microtyperTomzML.Rd man/mirrorPlot.Rd man/mirrorPlotDownload_UI.Rd man/mirrorPlotsSettings_UI.Rd man/mirrorPlots_Server.Rd man/mirrorPlots_UI.Rd man/modDendDotsMod_WellPanel.Rd man/modDendLabels_WellPanel.Rd man/modDendLines_WellPanel.Rd man/mquantSpecFromSQL.Rd man/multipleMaldiPlates.Rd man/parseDelimitedMS.Rd man/path_sanitize.Rd man/pcaCalculation.Rd man/pcoaCalculation.Rd man/peakBinner.Rd man/peakRetentionSettings_Server.Rd man/peakRetentionSettings_UI.Rd man/plateMapUI.Rd man/platemod.Rd man/plotHier.Rd man/plotly_3d_scatter.Rd man/popup3.Rd man/popup4.Rd man/popupPlotTsne_UI.Rd man/popupPlotTsne_server.Rd man/popupPlot_UI.Rd man/popupPlot_server.Rd man/processMZML.Rd man/processProteinSpectra.Rd man/processSmallMolSpectra.Rd man/processXMLIndSpectra.Rd man/proteinPeaksToMatrix.Rd man/readAcquFile.Rd man/runDendDots.Rd man/run_app.Rd man/sampMeta.Rd man/sampMetaOutput.Rd man/sampleChooser_UI.Rd man/sampleChooser_server.Rd man/selectDirectory_Server.Rd man/selectDirectory_UI.Rd man/selectInjections_UI.Rd man/selectInjections_server.Rd man/serial.Rd man/serializeXML.Rd man/smMANPlot_UI.Rd man/smallMolDFtoNetwork.Rd man/smallMolDendrogram_UI.Rd man/smallmirrorPlotsSampleSelect_UI.Rd man/smallmirrorPlots_Server.Rd man/smallmirrorPlots_UI.Rd man/spectraProcessingFunction.Rd man/spectrumMatrixToMALDIqaunt.Rd man/sqlCreate_version.Rd man/sqlTableArchitecture.Rd man/sql_CreateIndividualSpectra.Rd man/sql_CreateVersionTable.Rd man/sql_CreatemassTable.Rd man/sql_CreatemetaData.Rd man/sql_CreatexmlTable.Rd man/startingFromBrukerFlex.Rd man/startingFromMZ.Rd man/subtractMatrixBlank.Rd man/transferToNewDB_UI.Rd man/transferToNewDB_server.Rd man/tsneCalculation.Rd man/tsneUiPop.Rd man/ui_proteinClustering.Rd man/ui_smallMolMan.Rd man/updateCollapse.Rd man/updateMeta_UI.Rd man/updateMeta_server.Rd method.md tests/testthat.R tests/testthat/test-a.R
chasemc/tempRepo documentation built on April 8, 2019, 10:22 p.m.