Files in protViz/SRMService
Report Quantitative Mass Spectrometry Data
.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/A_dataset_docu.R
R/Grp2Analysis.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/eb.fit.R
R/limmaHelpers.R
R/plotNicelyTransitions.R
R/readMaxQuant.R
R/transitionCorrelations.R
R/zzz.R
README.md
SRMService.Rproj
_config.yml
data/correlatedPeptideList.rda
data/genericQuantMatrixGRP2.rda
data/grp2PullDownExample.rda
data/mqQuantMatrixGRP2.rda
inst/OneToOneAnalysis/MQ_sampleQC_overview.Rnw
inst/OneToOneAnalysis/Run_1To1_oldStyle.R
inst/OneToOneAnalysis/fgcz_MQ_QC_report.Rnw
inst/OneToOneAnalysis/images/LFQ_QC_workflow.pdf
inst/OneToOneAnalysis/images/LFQ_QC_workflow.png
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/exec/qcApplication.bat
inst/exec/startserver.bat
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/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/summary.txt
inst/samples/maxquant_txt/twoGroup3Reps.zip
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/skylineData.rda
man/.gitignore
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/genericQuantMatrixGRP2.Rd
man/getConditionColumns.Rd
man/getIDLabels.Rd
man/getIntensities.Rd
man/getPVals.Rd
man/getRequiredColumns.Rd
man/grp2PullDownExample.Rd
man/mergeLimmEBayesResult.Rd
man/mqQuantMatrixGRP2.Rd
man/multigroupEBaysQvalue.Rd
man/piwotPiw.Rd
man/plotNicely.Rd
man/proteinColumns.Rd
man/remap_PD_ProteinTable.Rd
man/transitionCorrelations.Rd
man/transitionCorrelationsJack.Rd
tests/testthat.R
tests/testthat/test-limmahelpers.R
tests/testthat/test-renderReports.R
vignettes/.gitignore
vignettes/.install_extras
vignettes/Empty.Rmd
vignettes/Grp2Analysis.Rmd
vignettes/Grp2Analysis_MissingInOneCondition.Rmd
vignettes/Grp2PullDownExample.Rmd
vignettes/bibliography.bib
vignettes/introduction-to-service.Rmd
