Files in chasemc/IDBacApp
MALDI-TOF MS Protien and Small Molecule Analysis
.Rbuildignore
.gitattributes
.gitignore
.travis.yml
DESCRIPTION
IDBac_App.Rproj
LICENSE.md
NAMESPACE
NEWS.md
R/0_current_database_version.R
R/app_run_app.R
R/app_server.R
R/app_ui.R
R/fct_assembleMirrorPlots.R
R/fct_availableSampleNames.R
R/fct_bootstrap.R
R/fct_chooseDirectory.R
R/fct_colored_Dots.R
R/fct_convertBruker.R
R/fct_delete_samples.R
R/fct_dendrogramCreator.R
R/fct_dendrogramModifiers.R
R/fct_distanceMatrix.R
R/fct_extractBrukerAcqInfo.R
R/fct_findIdbacHomeFolder.R
R/fct_findMSconvert.R
R/fct_findMissingSampleMapIds.R
R/fct_getSmallPeaksFromBrush.R
R/fct_getSubTrees.R
R/fct_idbacRetrievePeaksFromPool.R
R/fct_idbac_double_from_raw_compressed.R
R/fct_idbac_getSpectra.R
R/fct_idbac_get_peaks.R
R/fct_labelsFromBrushedDendrogram.R
R/fct_mergeDb.R
R/fct_metadataFromId.R
R/fct_mirrorPlots.R
R/fct_multidimensionalAnalyses.R
R/fct_networkFromDF.R
R/fct_normalizeSpectrumIntensity.R
R/fct_parseDelimitedMS.R
R/fct_parseMicrotyper.R
R/fct_pathSanitize.R
R/fct_peakFuzzifier.R
R/fct_plotly_3d_scatter.R
R/fct_prioritizer.R
R/fct_processMZML.R
R/fct_processXMLIndSpectra.R
R/fct_proteinPeaksToMatrix.r
R/fct_proteoWizConvert.R
R/fct_readBrukerAcqus.R
R/fct_readBrukerAcqusFile.r
R/fct_runDendDots.R
R/fct_smallMolDFtoNetwork.R
R/fct_spectraProcessingFunction.r
R/fct_spectraToPeaks.R
R/fct_subtractMatrixBlank.R
R/fct_updateIdbac.R
R/module_MANS.R
R/module_ModifyDendrogramLabels.R
R/module_ModifyDendrogramLines.R
R/module_appendToDendrogramLabels.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_dend_and_dots.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_news.R
R/module_plateMap.R
R/module_plotDendrogram.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/onLoad.R
R/searchNCBI.R
R/sql_connect.R
R/sql_copyToNewDatabase.r
R/sql_create_database.R
R/sql_dbCreators.R
R/sql_db_version.R
R/sql_exportmzML.R
R/sql_getDatabaseVersion.R
R/sql_insertMetadataColumns.R
R/sql_retrieveAllStrainIds.r
R/sql_spectrumMatrixToMALDIqaunt.R
R/sql_sqlTableArchitecture.r
R/sql_updateDatabaseVersion.R
R/ui_MAN.R
R/ui_chooserInput.r
R/ui_colorPicker.R
R/ui_popups.R
R/ui_proteinClustering.R
R/ui_shinyBS.R
R/utils-pipe.R
R/utils.R
README.md
inst/app/server.R
inst/app/ui.R
inst/prioritization_report.Rmd
inst/www/GitHub.png
inst/www/IDBac_Computer_SVG_300DPI.png
inst/www/Multi-MALDI-Plate.png
inst/www/Single-MALDI-Plate.png
inst/www/SmallAppIcon3.ico
inst/www/WorkingDirectory.png
inst/www/WorkingDirectory_ReAnalysis.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
inst/www/cssloader/assets/spinner.css
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
inst/www/cssloader/css-loaders/css/fallback.css
inst/www/cssloader/css-loaders/css/load1.css
inst/www/cssloader/css-loaders/css/load2.css
inst/www/cssloader/css-loaders/css/load3.css
inst/www/cssloader/css-loaders/css/load4.css
inst/www/cssloader/css-loaders/css/load5.css
inst/www/cssloader/css-loaders/css/load6.css
inst/www/cssloader/css-loaders/css/load7.css
inst/www/cssloader/css-loaders/css/load8.css
inst/www/cssloader/css-loaders/images/css-loaders-screenshot.jpg
inst/www/cssloader/css-loaders/less/fallback.less
inst/www/cssloader/css-loaders/less/load1.less
inst/www/cssloader/css-loaders/less/load2.less
inst/www/cssloader/css-loaders/less/load3.less
inst/www/cssloader/css-loaders/less/load4.less
inst/www/cssloader/css-loaders/less/load5.less
inst/www/cssloader/css-loaders/less/load6.less
inst/www/cssloader/css-loaders/less/load7.less
inst/www/cssloader/css-loaders/less/load8.less
inst/www/cssloader/css-loaders/package.json
inst/www/cssloader/css-loaders/sass/fallback.scss
inst/www/cssloader/css-loaders/sass/load1.scss
inst/www/cssloader/css-loaders/sass/load2.scss
inst/www/cssloader/css-loaders/sass/load3.scss
inst/www/cssloader/css-loaders/sass/load4.scss
inst/www/cssloader/css-loaders/sass/load5.scss
inst/www/cssloader/css-loaders/sass/load6.scss
inst/www/cssloader/css-loaders/sass/load7.scss
inst/www/cssloader/css-loaders/sass/load8.scss
inst/www/icon_svg.svg
inst/www/styles.css
man/MAN_Server.Rd
man/addAttribs.Rd
man/addClass.Rd
man/app_server.Rd
man/app_ui.Rd
man/appendDendLabsUI.Rd
man/as.binary.matrix.hclust.Rd
man/assembleMirrorPlots.Rd
man/baserMirrorPlot.Rd
man/bootlabels.Rd
man/bootstrap.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/colorBlindPalette.Rd
man/colorMANBy_UI.Rd
man/colorPicker.Rd
man/colordendLabelsUI.Rd
man/colordendLinesUI.Rd
man/colored_dots.Rd
man/compress.Rd
man/controlBrukerDisplay.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_dbDetach.Rd
man/copyDB_setupMeta.Rd
man/copyToNewDatabase.Rd
man/copyingDbPopup.Rd
man/createFuzzyVector.Rd
man/createFuzzyVectorUnit.Rd
man/createMetaSQL.Rd
man/createNewSQLITEdb.Rd
man/createSpectraSQL.Rd
man/createXMLSQL.Rd
man/current_db_version.Rd
man/databaseSelector_UI.Rd
man/databaseSelector_server.Rd
man/databaseTabServer.Rd
man/databaseTabUI.Rd
man/databaseTabUIFunc.Rd
man/db_from_bruker.Rd
man/db_from_mzml.Rd
man/decompress.Rd
man/delim_to_mzml.Rd
man/dendDotsServer.Rd
man/dendDotsUI.Rd
man/dendrogramActionsUI.Rd
man/dendrogramCreator.Rd
man/dendrogramCreatorUI.Rd
man/deserial.Rd
man/displayMissingProteinUI.Rd
man/distMatrix.Rd
man/dot-calculateMatches.Rd
man/dot-checkPool.Rd
man/dot-clust.Rd
man/dot-copy_db.Rd
man/dot-db_path_from_pool.Rd
man/dot-download_idbac_exe.Rd
man/dot-getLatestStableVersionPage.Rd
man/dot-getSmallPeaksFromBrush.Rd
man/dot-get_one_subtree.Rd
man/dot-grepAcquDoubleValue.Rd
man/dot-grepAcquValue.Rd
man/dot-parse_json_peaks.Rd
man/dot-resample.Rd
man/dot-retrieve_peaks_from_pool.Rd
man/dot-sampleName.Rd
man/dot-scale_ppm.Rd
man/dot-text.coord.hclust.Rd
man/double_from_raw_compressed.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/extractBrukerAcquistionInfo.Rd
man/extractHPCConstants.Rd
man/findIdbacHome.Rd
man/findMSconvert.Rd
man/findMissingSampleMapIds.Rd
man/find_mz_files.Rd
man/getAttribs.Rd
man/getMicrotyperFiles.Rd
man/getOS.Rd
man/get_subtrees.Rd
man/hashR.Rd
man/idbac_available_samples.Rd
man/idbac_connect.Rd
man/idbac_create.Rd
man/idbac_db_version.Rd
man/idbac_dendrogram_creator.Rd
man/idbac_get_metadata.Rd
man/idbac_get_peaks.Rd
man/idbac_get_spectra.Rd
man/idbac_update_db.Rd
man/insertIntoIndividualSpectra.Rd
man/insertIntoMassTable.Rd
man/insertMetadataColumns.Rd
man/labelsFromBrushedDendrogram.Rd
man/manPageProtDend_Server.Rd
man/manPageProtDend_UI.Rd
man/map384Well.Rd
man/merge_idbac_experiments.Rd
man/microtyperTomzML.Rd
man/mirrorPlot.Rd
man/mirrorPlotDownload_UI.Rd
man/mirrorPlotsSettings_UI.Rd
man/mirrorPlots_Server.Rd
man/mirrorPlots_UI.Rd
man/modAppendDendLabels_WellPanel.Rd
man/modDendDotsMod_WellPanel.Rd
man/modDendLabels_WellPanel.Rd
man/modDendLines_WellPanel.Rd
man/modularityClustering.Rd
man/mquant_bin.Rd
man/multipleMaldiPlates.Rd
man/networkFromDF.Rd
man/newUpdate.Rd
man/new_version_check.Rd
man/normalizeSpectrumIntensity.Rd
man/nulledMap384Well.Rd
man/pcaCalculation.Rd
man/pcoaCalculation.Rd
man/peakRetentionSettings_Server.Rd
man/peakRetentionSettings_UI.Rd
man/pipe.Rd
man/plateMapUI.Rd
man/platemod.Rd
man/plotDendrogram.Rd
man/plotHier.Rd
man/plotly_3d_scatter.Rd
man/poolToCon.Rd
man/popup3.Rd
man/popup4.Rd
man/popupPlotTsne_UI.Rd
man/popupPlotTsne_server.Rd
man/popupPlot_UI.Rd
man/popupPlot_server.Rd
man/prioritizer.Rd
man/processProteinSpectra.Rd
man/processSmallMolSpectra.Rd
man/processXMLIndSpectra.Rd
man/proteinPeaksToMatrix.Rd
man/proteoWizConvert.Rd
man/readAcqusFile.Rd
man/readBrukerAcqus.Rd
man/retrieveAllStrainIds.Rd
man/runDendDots.Rd
man/run_app.Rd
man/run_microtyperTomzML.Rd
man/sampleChooser_UI.Rd
man/sampleChooser_server.Rd
man/sampleMapViewer.Rd
man/sampleMaptoDF.Rd
man/sanitize.Rd
man/saveNetSVG.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/smallMolDendrogram_UI.Rd
man/small_maldiquant_to_network.Rd
man/smallmirrorPlotsSampleSelect_UI.Rd
man/smallmirrorPlots_Server.Rd
man/smallmirrorPlots_UI.Rd
man/spectraProcessingFunction.Rd
man/spectrumMatrixToMALDIqaunt.Rd
man/sql_create_locale_table.Rd
man/sql_create_massindex_table.Rd
man/sql_create_metadata_table.Rd
man/sql_create_spectra_table.Rd
man/sql_create_version_table.Rd
man/sql_create_xml_table.Rd
man/sql_fill_locale_table.Rd
man/sql_fill_version_table.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
man/update_idbac_modal.Rd
tests/testthat.R
tests/testthat/Rplots.pdf
tests/testthat/test-.R
tests/testthat/test-00_create_database.R
tests/testthat/test-01_create_database.R
tests/testthat/test-02_createfuzzyvector.R
tests/testthat/test-bootstrap.R
tests/testthat/test-brukerToMzml_popup.R
tests/testthat/test-colored_dots.R
tests/testthat/test-colorpalette.R
tests/testthat/test-controlBrukerDisplay.R
tests/testthat/test-copyDB_setupMeta.R
tests/testthat/test-copy_db.R
tests/testthat/test-databasetransfer.R
tests/testthat/test-db_path_from_pool.R
tests/testthat/test-db_update.R
tests/testthat/test-dbcreators.R
tests/testthat/test-distMatrix.R
tests/testthat/test-findIdbacHome.R
tests/testthat/test-findMSconvert.R
tests/testthat/test-findmissingsamplemapids.R
tests/testthat/test-getMicrotyperFiles.R
tests/testthat/test-getPeakData.R
tests/testthat/test-hashr.R
tests/testthat/test-insertlocale.R
tests/testthat/test-labelsfrombrusheddendrogram.R
tests/testthat/test-map384well.R
tests/testthat/test-mirrorplots.R
tests/testthat/test-module_databasetab.R
tests/testthat/test-module_dendrogram.R
tests/testthat/test-module_tsne.R
tests/testthat/test-networkCreators.R
tests/testthat/test-parseDelimitedMS.R
tests/testthat/test-pathsanitize.R
tests/testthat/test-plotly_3d_scatter.R
tests/testthat/test-readacqufile.R
tests/testthat/test-runapp.R
tests/testthat/test-samplemapviewer.R
tests/testthat/test-spectrummatrixtomaldiqaunt.R
tests/testthat/test-sqlTableArchitecture.R
tests/testthat/test-sql_CreateIndividualSpectra.R
tests/testthat/test-sql_CreatemassTable.R
tests/testthat/test-sql_CreatexmlTable.R
tests/testthat/test-subtree.R
tests/testthat/test-utils.R
