Files in cbielow/PTXQC
Quality Report Generation for MaxQuant and mzTab Results

.Rbuildignore
.gitignore
.travis.yml
CODE_OF_CONDUCT.md CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS
PTXQC.Rproj
R/FilenameMapper.R R/MQDataReader.R
R/MzQC_classes.R
R/MzTabReader.R R/PTXQC-package.R R/YAMLClass.R R/createReport.R R/createYaml.R R/fcn_MQ.R R/fcn_MQalign.R R/fcn_PCA.R R/fcn_QCHeat.R R/fcn_misc.R R/fcn_miscGGplot.R R/fcn_mqpar.R R/fcn_plots.R R/fcn_qualities.R R/modsToTable.R R/modsToTableByRaw.R R/mzQC.R R/pkg_internal.R R/plot_peptideMods.R R/qcMetric.R R/qcMetric_EVD.R R/qcMetric_EVD_modTable.R R/qcMetric_MSMS.R R/qcMetric_MSMSScans.R R/qcMetric_PAR.R R/qcMetric_PG.R R/qcMetric_SM.R README.md
docs/404.html
docs/CODE_OF_CONDUCT.html
docs/CONTRIBUTING.html
docs/LICENSE-text.html
docs/articles/DragNDrop_Action.png
docs/articles/DragNDrop_BatWindow.png
docs/articles/PTXQC-Basic_Guide_for_R_users.html
docs/articles/PTXQC-CustomizeReport.html
docs/articles/PTXQC-DragNDrop.html
docs/articles/PTXQC-FAQ.html
docs/articles/PTXQC-Input_And_Output_Data.html
docs/articles/PTXQC-ListOfMetrics.html
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/CV.html
docs/reference/FilenameMapper-class.html
docs/reference/LCS.html
docs/reference/LCSn.html
docs/reference/MQDataReader-class.html
docs/reference/MzTabReader-class.html
docs/reference/PTXQC-package.html
docs/reference/PTXQC.html
docs/reference/QCMetaFilenames.html
docs/reference/RSD.html
docs/reference/RTalignmentTree.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/Rplot005.png
docs/reference/Rplot006.png
docs/reference/ScoreInAlignWindow.html
docs/reference/YAMLClass-class.html
docs/reference/alignmentCheck.html
docs/reference/appendEnv.html
docs/reference/assembleMZQC.html
docs/reference/assignBlocks.html
docs/reference/boxplotCompare.html
docs/reference/brewer.pal.Safe.html
docs/reference/byX.html
docs/reference/byXflex.html
docs/reference/checkEnglishLocale.html
docs/reference/computeMatchRTFractions.html
docs/reference/correctSetSize.html
docs/reference/createReport.html
docs/reference/createYaml.html
docs/reference/darken.html
docs/reference/del0.html
docs/reference/delLCP.html
docs/reference/delLCS.html
docs/reference/findAlignReference.html
docs/reference/fixCalibration.html
docs/reference/flattenList.html
docs/reference/getAbundanceClass.html
docs/reference/getECDF-1.png
docs/reference/getECDF.html
docs/reference/getFileEncoding.html
docs/reference/getFragmentErrors.html
docs/reference/getHTMLTable.html
docs/reference/getMQPARValue.html
docs/reference/getMaxima.html
docs/reference/getMetaData.html
docs/reference/getMetricsObjects.html
docs/reference/getPCA.html
docs/reference/getPeptideCounts.html
docs/reference/getProteinCounts.html
docs/reference/getQCHeatMap.html
docs/reference/getReportFilenames.html
docs/reference/getRunQualityTemplate.html
docs/reference/ggAxisLabels.html
docs/reference/ggText.html
docs/reference/grapes-plus-grapes.html
docs/reference/grepv.html
docs/reference/idTransferCheck.html
docs/reference/inMatchWindow.html
docs/reference/index.html
docs/reference/lcpCount.html
docs/reference/lcsCount.html
docs/reference/longestCommonPrefix.html
docs/reference/longestCommonSuffix.html
docs/reference/modsToTable.html
docs/reference/modsToTableByRaw.html
docs/reference/mosaicize.html
docs/reference/pasten.html
docs/reference/pastet.html
docs/reference/peakSegmentation.html
docs/reference/peakWidthOverTime-1.png
docs/reference/peakWidthOverTime.html
docs/reference/plotTable-1.png
docs/reference/plotTable.html
docs/reference/plotTableRaw.html
docs/reference/plot_CalibratedMSErr-1.png
docs/reference/plot_CalibratedMSErr.html
docs/reference/plot_Charge-1.png
docs/reference/plot_Charge.html
docs/reference/plot_ContEVD-1.png
docs/reference/plot_ContEVD-2.png
docs/reference/plot_ContEVD.html
docs/reference/plot_ContUser-1.png
docs/reference/plot_ContUser.html
docs/reference/plot_ContUserScore-1.png
docs/reference/plot_ContUserScore.html
docs/reference/plot_ContsPG-1.png
docs/reference/plot_ContsPG.html
docs/reference/plot_CountData-1.png
docs/reference/plot_CountData.html
docs/reference/plot_DataOverRT-1.png
docs/reference/plot_DataOverRT.html
docs/reference/plot_IDRate-1.png
docs/reference/plot_IDRate.html
docs/reference/plot_IDsOverRT-1.png
docs/reference/plot_IDsOverRT.html
docs/reference/plot_IonInjectionTimeOverRT-1.png
docs/reference/plot_IonInjectionTimeOverRT.html
docs/reference/plot_MBRAlign-1.png
docs/reference/plot_MBRAlign.html
docs/reference/plot_MBRIDtransfer-1.png
docs/reference/plot_MBRIDtransfer.html
docs/reference/plot_MBRgain-1.png
docs/reference/plot_MBRgain.html
docs/reference/plot_MS2Decal-1.png
docs/reference/plot_MS2Decal.html
docs/reference/plot_MS2Oversampling-1.png
docs/reference/plot_MS2Oversampling.html
docs/reference/plot_MissedCleavages-1.png
docs/reference/plot_MissedCleavages.html
docs/reference/plot_RTPeakWidth-1.png
docs/reference/plot_RTPeakWidth.html
docs/reference/plot_RatiosPG-1.png
docs/reference/plot_RatiosPG.html
docs/reference/plot_ScanIDRate-1.png
docs/reference/plot_ScanIDRate.html
docs/reference/plot_TIC-1.png
docs/reference/plot_TIC.html
docs/reference/plot_TopN-1.png
docs/reference/plot_TopN.html
docs/reference/plot_TopNoverRT-1.png
docs/reference/plot_TopNoverRT.html
docs/reference/plot_UncalibratedMSErr-1.png
docs/reference/plot_UncalibratedMSErr.html
docs/reference/plot_peptideMods-1.png
docs/reference/plot_peptideMods.html
docs/reference/pointsPutX.html
docs/reference/print.PTXQC_table.html
docs/reference/printWithFooter.html
docs/reference/qcMetric-class-1.png
docs/reference/qcMetric-class-2.png
docs/reference/qcMetric-class-3.png
docs/reference/qcMetric-class-4.png
docs/reference/qcMetric-class-5.png
docs/reference/qcMetric-class-6.png
docs/reference/qcMetric-class.html
docs/reference/qcMetric_MSMSScans_TopNoverRT-class.html
docs/reference/qualBestKS.html
docs/reference/qualCentered.html
docs/reference/qualCenteredRef.html
docs/reference/qualGaussDev.html
docs/reference/qualHighest.html
docs/reference/qualLinThresh.html
docs/reference/qualMedianDist.html
docs/reference/qualUniform.html
docs/reference/read.MQ.html
docs/reference/renameFile.html
docs/reference/repEach.html
docs/reference/scale01linear.html
docs/reference/scale_x_discrete_reverse.html
docs/reference/scale_y_discrete_reverse.html
docs/reference/shortenStrings.html
docs/reference/simplifyNames.html
docs/reference/supCount.html
docs/reference/theme_blank.html
docs/reference/thinOut.html
docs/reference/thinOutBatch.html
docs/reference/wait_for_writable.html
docs/sitemap.xml
inst/CITATION
inst/dragNdrop/QC-dragdrop/_internal/compute_QC_report.R
inst/dragNdrop/QC-dragdrop/_internal/copy_complete_R_installation_folder_here.txt
inst/dragNdrop/QC-dragdrop/createQC_dragNdrop.bat
inst/dragNdrop/QC-dragdrop/createQC_dragNdrop_withYAML.bat
inst/dragNdrop/README.md inst/examples/README.md
inst/examples/example_IDoverRT.png
inst/examples/example_MBRalignment.png
inst/examples/example_heatmap.png
inst/examples/report_ecoli_small.mzQC
inst/examples/report_v1.1.0__txt_5files_withMatch-100min.html
inst/examples/report_v1.1.0__txt_5files_withMatch-100min.pdf inst/reportTemplate/PTXQC_report_template.Rmd
inst/reportTemplate/modes_UpSet.png
man/CV.Rd man/FilenameMapper-class.Rd man/LCS.Rd man/LCSn.Rd man/MQDataReader-class.Rd man/MzTabReader-class.Rd man/PTXQC-package.Rd man/QCMetaFilenames.Rd man/RSD.Rd man/RTalignmentTree.Rd man/ScoreInAlignWindow.Rd man/YAMLClass-class.Rd man/alignmentCheck.Rd man/appendEnv.Rd man/assembleMZQC.Rd man/assignBlocks.Rd man/boxplotCompare.Rd man/brewer.pal.Safe.Rd man/byX.Rd man/byXflex.Rd man/checkEnglishLocale.Rd man/computeMatchRTFractions.Rd man/correctSetSize.Rd man/createReport.Rd man/createYaml.Rd man/darken.Rd man/del0.Rd man/delLCP.Rd man/delLCS.Rd man/findAlignReference.Rd man/fixCalibration.Rd man/flattenList.Rd man/getAbundanceClass.Rd man/getECDF.Rd man/getFileEncoding.Rd man/getFragmentErrors.Rd man/getHTMLTable.Rd man/getMQPARValue.Rd man/getMaxima.Rd man/getMetaData.Rd man/getMetricsObjects.Rd man/getPCA.Rd man/getPeptideCounts.Rd man/getProteinCounts.Rd man/getQCHeatMap.Rd man/getReportFilenames.Rd man/getRunQualityTemplate.Rd man/ggAxisLabels.Rd man/ggText.Rd man/grapes-plus-grapes.Rd man/grepv.Rd man/idTransferCheck.Rd man/inMatchWindow.Rd man/lcpCount.Rd man/lcsCount.Rd man/longestCommonPrefix.Rd man/longestCommonSuffix.Rd man/modsToTable.Rd man/modsToTableByRaw.Rd man/mosaicize.Rd man/pasten.Rd man/pastet.Rd man/peakSegmentation.Rd man/peakWidthOverTime.Rd man/plotTable.Rd man/plotTableRaw.Rd man/plot_CalibratedMSErr.Rd man/plot_Charge.Rd man/plot_ContEVD.Rd man/plot_ContUser.Rd man/plot_ContUserScore.Rd man/plot_ContsPG.Rd man/plot_CountData.Rd man/plot_DataOverRT.Rd man/plot_IDRate.Rd man/plot_IDsOverRT.Rd man/plot_IonInjectionTimeOverRT.Rd man/plot_MBRAlign.Rd man/plot_MBRIDtransfer.Rd man/plot_MBRgain.Rd man/plot_MS2Decal.Rd man/plot_MS2Oversampling.Rd man/plot_MissedCleavages.Rd man/plot_RTPeakWidth.Rd man/plot_RatiosPG.Rd man/plot_ScanIDRate.Rd man/plot_TIC.Rd man/plot_TopN.Rd man/plot_TopNoverRT.Rd man/plot_UncalibratedMSErr.Rd man/plot_peptideMods.Rd man/pointsPutX.Rd man/print.PTXQC_table.Rd man/printWithFooter.Rd man/qcMetric-class.Rd man/qcMetric_MSMSScans_TopNoverRT-class.Rd man/qualBestKS.Rd man/qualCentered.Rd man/qualCenteredRef.Rd man/qualGaussDev.Rd man/qualHighest.Rd man/qualLinThresh.Rd man/qualMedianDist.Rd man/qualUniform.Rd man/read.MQ.Rd man/renameFile.Rd man/repEach.Rd man/scale01linear.Rd man/scale_x_discrete_reverse.Rd man/scale_y_discrete_reverse.Rd man/shortenStrings.Rd man/simplifyNames.Rd man/supCount.Rd man/theme_blank.Rd man/thinOut.Rd man/thinOutBatch.Rd man/wait_for_writable.Rd tests/testthat.R tests/testthat/test_computeQC.R tests/testthat/test_createYaml.R tests/testthat/test_misc.R tests/testthat/test_modsToTable.R tests/testthat/test_modsToTableByRaw.R tests/testthat/test_qcMetric.R tests/testthat/test_qualities.R
vignettes/DragNDrop_Action.png
vignettes/DragNDrop_BatWindow.png
vignettes/PTXQC-Basic_Guide_for_R_users.Rmd vignettes/PTXQC-CustomizeReport.Rmd vignettes/PTXQC-DragNDrop.Rmd vignettes/PTXQC-FAQ.Rmd vignettes/PTXQC-Input_And_Output_Data.Rmd vignettes/PTXQC-ListOfMetrics.Rmd
vignettes/readme.txt
cbielow/PTXQC documentation built on March 13, 2024, 5:08 a.m.