Files in protViz/SRMService
Performs Service SRM and LFQ analysis

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/Grp2Analysis.R R/MQProteinGroups.R R/MSStatsMappings.R R/PrepareRmdAnalysisEnv.R R/ProteinTable.R R/QCReport.R R/RequiredColumns.R R/SRMService.R R/ScaffoldHelpers.R R/TidyMS.R R/eb.fit.R R/fgcz.R R/hello.R R/limmaHelpers.R R/readMaxQuant.R R/transitionCorrelations.R R/zzz.R README.md
SRMService.Rproj
Sweave.sty
inst/OneToOneAnalysis/MQ_sampleQC_overview.Rnw
inst/OneToOneAnalysis/Run_1To1_oldStyle.R inst/OneToOneAnalysis/helpers/QprotMatrixFunctions_rn_V3.R inst/OneToOneAnalysis/images/LFQ_QC_workflow.pdf
inst/OneToOneAnalysis/images/Sweave.sty
inst/RunScripts/RUN_SRMPeptideProteinQC.R inst/RunScripts/RUN_VarSelection.R inst/RunScripts/Run_QuantQCReport.R inst/RunScripts/Run_QuantTwoGroupAnalysis.R inst/RunScripts/Run_SpecLWithProzor.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/QCReport.Rmd inst/reports/SRM_NormalizeByProteins.Rmd inst/reports/SRM_PeptideProteinQC.Rmd inst/reports/TestingCrossreferences.Rmd inst/reports/VariableSelection_GLM.Rmd inst/reports/VariableSelection_MultinomialLasso.Rmd inst/reports/VariableSelection_ROCSingleProtein.Rmd inst/reports/specLWithProzor.Rmd
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/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/output/annotationused.txt
inst/samples/proteinGroups/output/pValues.csv
inst/samples/proteinGroups/proteinGroups.txt
inst/samples/proteinGroups/proteinGroups2x4.txt
inst/samples/proteinGroups/proteinGroupsFailed.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/QCProteinReport-class.Rd man/RMD_LibraryGen_specLProzor.Rd man/RMD_QC1To1_Old.Rd man/RMD_Quant_2GrpAnalysis.Rd man/RMD_Quant_QCReport.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/eb.fit.Rd man/fixScaffoldQuantReport.Rd man/getConditionColumns.Rd man/getIDLabels.Rd man/getIntensities.Rd man/getPVals.Rd man/getRequiredColumns.Rd man/mergeLimmEBayesResult.Rd man/multigroupEBaysQvalue.Rd man/piwotPiw.Rd man/plotNicely.Rd man/proteinColumns.Rd man/summariseQValues.Rd man/tidyMQ_ProteinGroups.Rd man/transitionCorrelations.Rd man/transitionCorrelationsJack.Rd
qcApplication.bat
startserver.bat
test.yaml
protViz/SRMService documentation built on Jan. 15, 2018, 4:58 a.m.