Files in protViz/SRMService
Performs Service SRM and LFQ analysis

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/A_dataset_docu.R R/Grp2Analysis.R R/MQProteinGroups.R R/MSStatsMappings.R R/One2OneAnalysisHelpers.R R/PDProteins.R R/PrepareRmdAnalysisEnv.R R/QCReport.R R/R6_ProteinTable.R R/R6_ProteinVariableSelect.R R/RequiredColumns.R R/SRMService.R R/ScaffoldHelpers.R R/TidyMS.R R/eb.fit.R R/limmaHelpers.R R/plotNicelyTransitions.R R/readMaxQuant.R R/tidyMS_R6_AnalysisConfiguration.R R/transitionCorrelations.R R/zzz.R README.md
SRMService.Rproj
Sweave.sty
data/correlatedPeptideList.rda
inst/OneToOneAnalysis/MQ_sampleQC_overview.Rnw
inst/OneToOneAnalysis/Run_1To1_oldStyle.R inst/OneToOneAnalysis/images/LFQ_QC_workflow.pdf
inst/OneToOneAnalysis/images/Sweave.sty
inst/RunScripts/RUN_SRMPeptideProteinQC.R inst/RunScripts/RUN_VarSelection_Multinomial.R inst/RunScripts/Run_Generic_QuantTwoGroupAnalysis.R inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R inst/RunScripts/Run_PD_QuantTwoGroupAnalysis.R inst/RunScripts/Run_QuantQCReport.R inst/RunScripts/Run_SpecLWithProzor.R inst/RunScripts/Run_VarSelection_GLM.R
inst/figures/LFQBench1.jpg
inst/figures/LFQBench2.jpg
inst/figures/ROPECA.jpg
inst/figures/SREP-16-32328-T.R.zip
inst/figures/Swath2Stats.PNG
inst/figures/TAPROverviewImage.jpg
inst/figures/msQRobBenchmark.gif
inst/reports/Grp2Analysis.Rmd inst/reports/Grp2Analysis_Empty.Rmd inst/reports/Grp2Analysis_MissingInOneCondtion.Rmd inst/reports/LimmaAnalysis.Rmd inst/reports/QCReport.Rmd inst/reports/SRM_NormalizeByProteins.Rmd inst/reports/SRM_PeptideProteinQC.Rmd inst/reports/TestingCrossreferences.Rmd inst/reports/VariableSelection_GLM.Rmd inst/reports/VariableSelection_GLM_NV2.Rmd inst/reports/VariableSelection_MultinomialLasso.Rmd inst/reports/VariableSelection_ROCSingleProtein.Rmd inst/reports/specLWithProzor.Rmd
inst/samples/genericQuantMatrix/Generic_QuantMatrix.txt
inst/samples/immunoLongFormat.txt
inst/samples/maxquant_txt/MSQC1/evidence.txt
inst/samples/maxquant_txt/MSQC1/msms.txt
inst/samples/maxquant_txt/MSQC1/parameters.txt
inst/samples/maxquant_txt/MSQC1/peptides.txt
inst/samples/maxquant_txt/MSQC1/proteinGroups.txt
inst/samples/maxquant_txt/MSQC1/proteinGroups_FGCZ2grp_Intensity.txt
inst/samples/maxquant_txt/MSQC1/proteinGroups_withTicksFaked.txt
inst/samples/maxquant_txt/MSQC1/summary.txt
inst/samples/maxquant_txt/tiny/evidence.txt
inst/samples/maxquant_txt/tiny/msms.txt
inst/samples/maxquant_txt/tiny/peptides.txt
inst/samples/maxquant_txt/tiny/proteinGroups.txt
inst/samples/maxquant_txt/tiny/proteinGroups_FGCZ2grp_Intensity.txt
inst/samples/maxquant_txt/tiny/summary.txt
inst/samples/old_MQ_resultOverview_asExample.pdf inst/samples/proteinGroups/PullDownTest.R
inst/samples/proteinGroups/proteinGroups.txt
inst/samples/proteinGroups/proteinGroups2x4.txt
inst/samples/proteinGroups/proteinGroupsFailed.txt
inst/samples/proteinGroups/proteinGroupsPullDown.txt
inst/samples/toniSuomiPaper/Data/mcp.M114.044305-3.xlsx
inst/samples/toniSuomiPaper/RopecaOnly.R inst/samples/toniSuomiPaper/SREP-16-32328-T.R inst/shiny/2Group2Test/server.R inst/shiny/2Group2Test/ui.R inst/shiny/QCApp/server.R inst/shiny/QCApp/ui.R inst/shiny/Todo/Render.R inst/shiny/Todo/TODO.Rmd
inst/shiny/Todo/TODO.html
man/Annotation.Rd man/Grp2Analysis-class.Rd man/MQtoMSstatsFormat.Rd man/MSstatsMapping.Rd man/PeptideTable-class.Rd man/ProteinTable-class.Rd man/ProteinTableR6.Rd man/ProteinVariableSelect.Rd man/QCProteinReport-class.Rd man/RMD_LibraryGen_specLProzor.Rd man/RMD_MQ_Quant_2GrpAnalysis.Rd man/RMD_MQ_Quant_QCReport.Rd man/RMD_PD_Quant_2GrpAnalysis.Rd man/RMD_QC1To1_Old.Rd man/RMD_SRM_QC_Normalization.Rd man/RMD_VarSelection.Rd man/SRMService-class.Rd man/TransitionTable-class.Rd man/annotationColumns.Rd man/contrasts.fit.NA.Rd man/correlatedPeptideList.Rd man/eb.fit.Rd man/fgcz_render_One2OneReport.Rd man/fixScaffoldQuantReport.Rd man/fix_PD_inputFiles.Rd man/getConditionColumns.Rd man/getIDLabels.Rd man/getIntensities.Rd man/getPVals.Rd man/getRequiredColumns.Rd man/linePlotHierarchy_configuration.Rd man/linePlotHierarchy_default.Rd man/mergeLimmEBayesResult.Rd man/multigroupEBaysQvalue.Rd man/piwotPiw.Rd man/plotNicely.Rd man/proteinColumns.Rd man/remap_PD_ProteinTable.Rd man/summariseQValues.Rd man/summarizeProteins.Rd man/tidyMQ_Peptides.Rd man/tidyMQ_ProteinGroups.Rd man/transitionCorrelations.Rd man/transitionCorrelationsJack.Rd
qcApplication.bat
startserver.bat
test.yaml
tests/testthat.R tests/testthat/test_Annotation.R
protViz/SRMService documentation built on June 22, 2018, 10:24 a.m.