Files in phenomecentre/peakPantheR

Peak Picking and Annotation of High Resolution Experiments

CONTRIBUTIONS.md R/GUI_utils.R R/class_peakPantheRAnnotation.R R/curveFit_utils.R R/extractSignalRawData.R R/findTargetFeatures.R R/generateIonChromatogram.R R/getAcquisitionDatemzML.R R/getTargetFeatureStatistic.R R/initialize_peakPantheRAnnotation.R R/integrateFIR.R R/methods_peakPantheRAnnotation.R R/peakPantheR.R R/peakPantheR_ROIStatistics.R R/peakPantheR_loadAnnotationParamsCSV.R R/peakPantheR_parallelAnnotation.R R/peakPantheR_plotEICFit.R R/peakPantheR_plotPeakwidth.R R/peakPantheR_quickEIC.R R/peakPantheR_singleFileSearch.R R/peakPantheR_start_GUI.R R/plotAnnotationDiagnosticMultiplot.R R/plotEICDetectedPeakwidth.R R/plotHistogram.R R/rtCorrection_utils.R R/saveSingleFileMultiEIC.R R/valid_peakPantheRAnnotation.R R/zzz.R README.md inst/scripts/make_unittest_data.R inst/shiny-GUI/peakPantheR-App/server.R inst/shiny-GUI/peakPantheR-App/server/server_diagnostic.R inst/shiny-GUI/peakPantheR-App/server/server_export.R inst/shiny-GUI/peakPantheR-App/server/server_import.R inst/shiny-GUI/peakPantheR-App/server/server_results.R inst/shiny-GUI/peakPantheR-App/server/server_run.R inst/shiny-GUI/peakPantheR-App/ui.R inst/shiny-GUI/peakPantheR-App/ui/ui_about.R inst/shiny-GUI/peakPantheR-App/ui/ui_diagnostic.R inst/shiny-GUI/peakPantheR-App/ui/ui_export.R inst/shiny-GUI/peakPantheR-App/ui/ui_import.R inst/shiny-GUI/peakPantheR-App/ui/ui_results.R inst/shiny-GUI/peakPantheR-App/ui/ui_run.R man/EICs-peakPantheRAnnotation-method.Rd man/FIR-peakPantheRAnnotation-method.Rd man/ROI-peakPantheRAnnotation-method.Rd man/TIC-peakPantheRAnnotation-method.Rd man/acquisitionTime-peakPantheRAnnotation-method.Rd man/annotationDiagnosticMultiplot.Rd man/annotationDiagnosticPlots-peakPantheRAnnotation-method.Rd man/annotationParamsDiagnostic-peakPantheRAnnotation-method.Rd man/annotationTable-peakPantheRAnnotation-method.Rd man/annotation_diagnostic_multiplot_UI_helper.Rd man/annotation_fit_summary_UI_helper.Rd man/annotation_showMethod_UI_helper.Rd man/annotation_showText_UI_helper.Rd man/cpdID-peakPantheRAnnotation-method.Rd man/cpdMetadata-peakPantheRAnnotation-method.Rd man/cpdName-peakPantheRAnnotation-method.Rd man/dataPoints-peakPantheRAnnotation-method.Rd man/emgGaussian_guess.Rd man/emgGaussian_minpack.lm.Rd man/emgGaussian_minpack.lm_objectiveFun.Rd man/extractSignalRawData.Rd man/filename-peakPantheRAnnotation-method.Rd man/filepath-peakPantheRAnnotation-method.Rd man/findTargetFeatures.Rd man/fitCurve.Rd man/gaussian_cerf.Rd man/gaussian_erf.Rd man/generateIonChromatogram.Rd man/getAcquisitionDatemzML.Rd man/getTargetFeatureStatistic.Rd man/initialise_annotation_from_files_UI_helper.Rd man/integrateFIR.Rd man/is.peakPantheR_curveFit.Rd man/isAnnotated-peakPantheRAnnotation-method.Rd man/load_annotation_from_file_UI_helper.Rd man/nbCompounds-peakPantheRAnnotation-method.Rd man/nbSamples-peakPantheRAnnotation-method.Rd man/outputAnnotationDiagnostic-peakPantheRAnnotation-method.Rd man/outputAnnotationFeatureMetadata_UI_helper.Rd man/outputAnnotationParamsCSV-peakPantheRAnnotation-method.Rd man/outputAnnotationResult-peakPantheRAnnotation-method.Rd man/outputAnnotationSpectraMetadata_UI_helper.Rd man/peakFit-peakPantheRAnnotation-method.Rd man/peakPantheR.Rd man/peakPantheRAnnotation.Rd man/peakPantheR_ROIStatistics.Rd man/peakPantheR_applyRTCorrection.Rd man/peakPantheR_loadAnnotationParamsCSV.Rd man/peakPantheR_parallelAnnotation.Rd man/peakPantheR_plotEICFit.Rd man/peakPantheR_plotPeakwidth.Rd man/peakPantheR_quickEIC.Rd man/peakPantheR_singleFileSearch.Rd man/peakPantheR_start_GUI.Rd man/peakTables-peakPantheRAnnotation-method.Rd man/plotEICDetectedPeakwidth.Rd man/plotHistogram.Rd man/predictCurve.Rd man/prepare_advanced_target_parameters.Rd man/prepare_basic_target_parameters.Rd man/resetAnnotation-peakPantheRAnnotation-method.Rd man/resetFIR-peakPantheRAnnotation-method.Rd man/retentionTimeCorrection-peakPantheRAnnotation-method.Rd man/saveSingleFileMultiEIC.Rd man/skewedGaussian_guess.Rd man/skewedGaussian_minpack.lm.Rd man/skewedGaussian_minpack.lm_objectiveFun.Rd man/spectraMetadata-peakPantheRAnnotation-method.Rd man/spectraPaths_and_metadata_UI_helper.Rd man/spectra_metadata_colourScheme_UI_helper.Rd man/sub-peakPantheRAnnotation-ANY-ANY-ANY-method.Rd man/uROI-peakPantheRAnnotation-method.Rd man/uROIExist-peakPantheRAnnotation-method.Rd man/useFIR-peakPantheRAnnotation-method.Rd man/useUROI-peakPantheRAnnotation-method.Rd tests/testthat.R tests/testthat/test_annotationDiagnosticMultiplot.R tests/testthat/test_annotation_diagnostic_multiplot_UI_helper.R tests/testthat/test_annotation_fit_summary_UI_helper.R tests/testthat/test_annotation_showMethod_UI_helper.R tests/testthat/test_annotation_showText_UI_helper.R tests/testthat/test_centroid_continuum_reader.R tests/testthat/test_continuum_mode.R tests/testthat/test_emgGaussian_utils.R tests/testthat/test_extractSignalRawData.R tests/testthat/test_findTargetFeatures.R tests/testthat/test_fitCurve.R tests/testthat/test_generateIonChromatogram.R tests/testthat/test_getAcquisitionDatemzML.R tests/testthat/test_getTargetFeatureStatistic.R tests/testthat/test_initialise_annotation_from_files_UI_helper.R tests/testthat/test_integrateFIR.R tests/testthat/test_load_annotation_from_file_UI_helper.R tests/testthat/test_outputAnnotation_UI_helpers.R tests/testthat/test_peakPantheRAnnotation_accessor-method.R tests/testthat/test_peakPantheRAnnotation_annotationDiagnosticPlots-method.R tests/testthat/test_peakPantheRAnnotation_annotationParamsDiagnostic-method.R tests/testthat/test_peakPantheRAnnotation_class_initialize-method.R tests/testthat/test_peakPantheRAnnotation_extract-method.R tests/testthat/test_peakPantheRAnnotation_outputAnnotationDiagnostic-method.R tests/testthat/test_peakPantheRAnnotation_outputAnnotationParamsCSV-method.R tests/testthat/test_peakPantheRAnnotation_outputAnnotationResult-method.R tests/testthat/test_peakPantheRAnnotation_resetAnnotation-method.R tests/testthat/test_peakPantheRAnnotation_resetFIR-method.R tests/testthat/test_peakPantheRAnnotation_retentionTimeCorrection-method.R tests/testthat/test_peakPantheRAnnotation_show-method.R tests/testthat/test_peakPantheRAnnotation_validObject-method.R tests/testthat/test_peakPantheR_ROIStatistics.R tests/testthat/test_peakPantheR_applyRTCorrection.R tests/testthat/test_peakPantheR_loadAnnotationParamsCSV.R tests/testthat/test_peakPantheR_parallelAnnotation.R tests/testthat/test_peakPantheR_plotEICFit.R tests/testthat/test_peakPantheR_plotPeakwidth.R tests/testthat/test_peakPantheR_quickEIC.R tests/testthat/test_peakPantheR_singleFileSearch.R tests/testthat/test_plotEICDetectedPeakwidth.R tests/testthat/test_plotHistogram.R tests/testthat/test_predictCurve.R tests/testthat/test_saveSingleFileMultiEIC.R tests/testthat/test_skewedGaussian_utils.R tests/testthat/test_spectraPaths_and_metadata_UI_helper.R tests/testthat/test_spectra_metadata_colourScheme_UI_helper.R vignettes/getting-started.Rmd vignettes/parallel-annotation.Rmd vignettes/peakPantheR-GUI.Rmd vignettes/real-time-annotation.Rmd