Files in MeenaChoi/MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

.Rbuildignore

.github/pull_request_template.md

.github/workflows/codium-pr-agent.yml

.github/workflows/dry-run-build.yml

.gitignore

.travis.yml

DESCRIPTION

MSstats.Rproj

NAMESPACE

R/RcppExports.R R/SDRFconverter.R R/converters.R R/dataProcess.R R/dataProcessPlots.R R/designSampleSize.R R/groupComparison.R R/groupComparisonPlots.R R/groupComparisonQCPlots.R R/msstats-package.R R/quantification.R R/utils_censored.R R/utils_checks.R R/utils_dataprocess_plots.R R/utils_feature_selection.R R/utils_groupcomparison.R R/utils_groupcomparison_checks.R R/utils_groupcomparison_contrasts.R R/utils_groupcomparison_plots.R R/utils_imputation.R R/utils_normalize.R R/utils_output.R R/utils_plots_common.R R/utils_statistics.R R/utils_summarization.R R/utils_summarization_prepare.R README.md

_pkgdown.yml

appspec.yml

codecov.yml

data/.Rapp.history

data/DDARawData.RData

data/DDARawData.Skyline.RData

data/DIARawData.RData

data/SRMRawData.RData

data/example_SDRF.RData

docs/404.html

docs/articles/MSstats.html

docs/articles/index.html

docs/authors.html

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/ConditionPlot.pdf docs/reference/ConditionPlot_2.pdf docs/reference/ConditionPlot_3.pdf docs/reference/ConditionPlot_4.pdf

docs/reference/DDARawData.Skyline.html

docs/reference/DDARawData.html

docs/reference/DIARawData.html

docs/reference/DIAUmpiretoMSstatsFormat.html

docs/reference/Ex1_ComparisonPlot.pdf docs/reference/Ex1_ComparisonPlot_2.pdf docs/reference/Ex1_Heatmap.pdf docs/reference/Ex1_Heatmap_2.pdf docs/reference/Ex1_VolcanoPlot.pdf docs/reference/Ex1_VolcanoPlot_2.pdf docs/reference/Ex2_ComparisonPlot.pdf docs/reference/Ex2_ComparisonPlot_2.pdf docs/reference/Ex2_Heatmap.pdf docs/reference/Ex2_Heatmap_2.pdf docs/reference/Ex2_VolcanoPlot.pdf docs/reference/Ex2_VolcanoPlot_2.pdf

docs/reference/MSstatsContrastMatrix.html

docs/reference/MSstatsGroupComparison.html

docs/reference/MSstatsGroupComparisonOutput.html

docs/reference/MSstatsGroupComparisonSingleProtein.html

docs/reference/MSstatsHandleMissing.html

docs/reference/MSstatsMergeFractions.html

docs/reference/MSstatsNormalize.html

docs/reference/MSstatsPrepareForDataProcess.html

docs/reference/MSstatsPrepareForGroupComparison.html

docs/reference/MSstatsPrepareForSummarization.html

docs/reference/MSstatsSelectFeatures.html

docs/reference/MSstatsSummarizationOutput.html

docs/reference/MSstatsSummarize.html

docs/reference/MSstatsSummarizeSingleLinear.html

docs/reference/MSstatsSummarizeSingleTMP.html

docs/reference/MaxQtoMSstatsFormat.html

docs/reference/OpenMStoMSstatsFormat.html

docs/reference/OpenSWATHtoMSstatsFormat.html

docs/reference/PDtoMSstatsFormat.html

docs/reference/ProfilePlot.pdf docs/reference/ProfilePlot_2.pdf docs/reference/ProfilePlot_4.pdf docs/reference/ProfilePlot_6.pdf docs/reference/ProfilePlot_wSummarization.pdf docs/reference/ProfilePlot_wSummarization_2.pdf docs/reference/ProfilePlot_wSummarization_3.pdf docs/reference/ProfilePlot_wSummarization_4.pdf

docs/reference/ProgenesistoMSstatsFormat.html

docs/reference/QCPlot.pdf docs/reference/QCPlot_2.pdf docs/reference/QCPlot_3.pdf docs/reference/QCPlot_4.pdf docs/reference/QQPlot.pdf docs/reference/QQPlot_2.pdf docs/reference/ResidualPlot.pdf docs/reference/ResidualPlot_2.pdf

docs/reference/SRMRawData.html

docs/reference/SkylinetoMSstatsFormat.html

docs/reference/SpectronauttoMSstatsFormat.html

docs/reference/checkRepeatedDesign.html

docs/reference/dataProcess.html

docs/reference/dataProcessPlots.html

docs/reference/designSampleSize.html

docs/reference/designSampleSizePlots-1.png

docs/reference/designSampleSizePlots-2.png

docs/reference/designSampleSizePlots.html

docs/reference/dot-addCoverageInfo.html

docs/reference/dot-addModelInformation.html

docs/reference/dot-addModelVariances.html

docs/reference/dot-addNInformativeInfo.html

docs/reference/dot-addNoisyFlag.html

docs/reference/dot-addOutlierCutoff.html

docs/reference/dot-addOutlierInformation.html

docs/reference/dot-addSurvivalPredictions.html

docs/reference/dot-adjustLRuns.html

docs/reference/dot-calculateOutlierCutoff.html

docs/reference/dot-calculatePower.html

docs/reference/dot-calculateProteinVariance.html

docs/reference/dot-checkContrastMatrix.html

docs/reference/dot-checkDataProcessParams.html

docs/reference/dot-checkExperimentDesign.html

docs/reference/dot-checkGCPlotsInput.html

docs/reference/dot-checkGroupComparisonInput.html

docs/reference/dot-checkSingleFeature.html

docs/reference/dot-checkSingleLabelProteins.html

docs/reference/dot-checkSingleSubject.html

docs/reference/dot-checkTechReplicate.html

docs/reference/dot-checkUnProcessedDataValidity.html

docs/reference/dot-countInformative.html

docs/reference/dot-countMissingPercentage.html

docs/reference/dot-documentFunction.html

docs/reference/dot-finalizeInput.html

docs/reference/dot-finalizeLinear.html

docs/reference/dot-finalizeTMP.html

docs/reference/dot-fitHuber.html

docs/reference/dot-fitLinearModel.html

docs/reference/dot-fitModelForGroupComparison.html

docs/reference/dot-fitModelSingleProtein.html

docs/reference/dot-fitTukey.html

docs/reference/dot-flagLowCoverage.html

docs/reference/dot-flagUninformativeSingleLabel.html

docs/reference/dot-getAllComparisons.html

docs/reference/dot-getContrast.html

docs/reference/dot-getContrastLabels.html

docs/reference/dot-getEmptyComparison.html

docs/reference/dot-getFeatureVariances.html

docs/reference/dot-getMedian.html

docs/reference/dot-getMedianSigmaSubject.html

docs/reference/dot-getMin.html

docs/reference/dot-getModelParameters.html

docs/reference/dot-getNonMissingFilter.html

docs/reference/dot-getNonMissingFilterStats.html

docs/reference/dot-getNumSample.html

docs/reference/dot-getSingleProteinForProfile.html

docs/reference/dot-getVarComponent.html

docs/reference/dot-getWideTable.html

docs/reference/dot-getYaxis.html

docs/reference/dot-handleEmptyConditions.html

docs/reference/dot-handleSingleContrast.html

docs/reference/dot-isSummarizable.html

docs/reference/dot-logDatasetInformation.html

docs/reference/dot-logMissingness.html

docs/reference/dot-logSingleLabeledProteins.html

docs/reference/dot-logSummaryStatistics.html

docs/reference/dot-makeComparison.html

docs/reference/dot-makeConditionPlot.html

docs/reference/dot-makeFactorColumns.html

docs/reference/dot-makeHeatmap.html

docs/reference/dot-makeProfilePlot.html

docs/reference/dot-makeQCPlot.html

docs/reference/dot-makeSummaryProfilePlot.html

docs/reference/dot-makeVolcano.html

docs/reference/dot-nicePrint.html

docs/reference/dot-normalizeGlobalStandards.html

docs/reference/dot-normalizeMedian.html

docs/reference/dot-normalizeQuantile.html

docs/reference/dot-onLoad.html

docs/reference/dot-plotComparison.html

docs/reference/dot-plotHeatmap.html

docs/reference/dot-plotVolcano.html

docs/reference/dot-preProcessIntensities.html

docs/reference/dot-prepareForDataProcess.html

docs/reference/dot-prepareLinear.html

docs/reference/dot-prepareSingleProteinForGC.html

docs/reference/dot-prepareSummary.html

docs/reference/dot-prepareTMP.html

docs/reference/dot-quantileNormalizationSingleLabel.html

docs/reference/dot-replaceZerosWithNA.html

docs/reference/dot-runTukey.html

docs/reference/dot-saveSessionInfo.html

docs/reference/dot-saveTable.html

docs/reference/dot-selectHighQualityFeatures.html

docs/reference/dot-selectTopFeatures.html

docs/reference/dot-setCensoredByThreshold.html

docs/reference/dot-updateColumnsForProcessing.html

docs/reference/dot-updateUnequalVariances.html

docs/reference/getProcessed.html

docs/reference/getSamplesInfo.html

docs/reference/getSelectedProteins.html

docs/reference/groupComparison.html

docs/reference/groupComparisonPlots-1.png

docs/reference/groupComparisonPlots-2.png

docs/reference/groupComparisonPlots.html

docs/reference/index.html

docs/reference/makePeptidesDictionary.html

docs/reference/modelBasedQCPlots.html

docs/reference/quantification.html

docs/reference/savePlot.html

docs/reference/theme_msstats.html

inst/CITATION

inst/NEWS.rd

inst/scripts/after_install.sh

inst/tinytest/annotations/annot_diau.csv

inst/tinytest/annotations/annot_os.csv

inst/tinytest/annotations/annot_pd.csv

src/.gitignore

src/Makevars

src/Makevars.win

src/RcppExports.cpp

src/common.cpp

src/common.h

src/comparison_contrasts.cpp

src/linear_summary.cpp

src/median_polish.cpp

tests/tinytest.R vignettes/MSstats.Rmd vignettes/MSstatsWorkflow.Rmd

MeenaChoi/MSstats documentation built on Nov. 10, 2024, 2:43 p.m.

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MeenaChoi/MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Files in MeenaChoi/MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

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MeenaChoi/MSstats Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Files in MeenaChoi/MSstats Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

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MeenaChoi/MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Files in MeenaChoi/MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments