Files in phenomecentre/peakPantheR
Peak Picking and Annotation of High Resolution Experiments
.Rbuildignore
.covrignore
.github/.gitignore
.github/workflows/check-bioc-devel.yml
.github/workflows/check-bioc.yml
.gitignore
CONTRIBUTIONS.md
DESCRIPTION
NAMESPACE
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
_pkgdown.yml
inst/CITATION
inst/NEWS
inst/extdata/test_fakemzML.mzML
inst/scripts/make_unittest_data.R
inst/shiny-GUI/peakPantheR-App/data/about.html
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
inst/shiny-GUI/peakPantheR-App/www/annot_progress.gif
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/figures/01-import_RData.png
man/figures/02-import_CSV.png
man/figures/03-Run_annotation.png
man/figures/04-Diagnostic_statistics.png
man/figures/05-Diagnostic_updateUROIFIR.png
man/figures/06-Diagnostic_plot.png
man/figures/07-Results_Overall.png
man/figures/08-Results_byFeature.png
man/figures/09-Results_bySample.png
man/figures/10-Export.png
man/figures/example-UI.png
man/figures/parallelAnnotation.png
man/figures/parallelAnnotation_procedure.png
man/figures/parallel_annotation_diagnostic_cpd1.png
man/figures/peakPantheR-logo.png
man/figures/singleFileSearch_EICsPlot.png
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
vignettes/references.bib
