├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── NormalyzerDE.R ├── NormalyzerDataset.R ├── NormalyzerEvaluationResults.R ├── NormalyzerResults.R ├── NormalyzerStatistics.R ├── analyzeResults.R ├── calculateStatistics.R ├── data.R ├── generatePlots.R ├── higherOrderNormMethods.R ├── inputVerification.R ├── normMethods.R ├── outputUtils.R ├── preparsers.R ├── printMeta.R ├── printPlots.R └── utils.R ├── README.md ├── data ├── example_data.rda ├── example_data_only_values.rda ├── example_data_only_values_small.rda ├── example_data_small.rda ├── example_design.rda ├── example_design_small.rda ├── example_stat_data.rda ├── example_stat_summarized_experiment.rda ├── example_summarized_experiment.rda ├── example_wide_data.rda └── example_wide_design.rda ├── inst ├── CITATION ├── extdata │ ├── data.tsv │ ├── design.tsv │ ├── design_tech_rep.tsv │ ├── four_col_data.tsv │ ├── four_col_design.tsv │ ├── mq_peptides_100.txt │ ├── mq_proteinGroups_100.txt │ ├── stat_runs │ │ ├── batch │ │ │ ├── Norm-stats-report-batch.pdf │ │ │ └── batch_stats.tsv │ │ ├── log2 │ │ │ ├── Norm-stats-report-log2.pdf │ │ │ └── log2_stats.tsv │ │ ├── multiple_comps │ │ │ ├── Norm-stats-report-multiple_comps.pdf │ │ │ └── multiple_comps_stats.tsv │ │ ├── normal │ │ │ ├── Norm-stats-report-unit_test_run_stat.pdf │ │ │ └── normal_stats.tsv │ │ ├── techrep │ │ │ ├── Norm-stats-report-techrep.pdf │ │ │ └── techrep_stats.tsv │ │ └── welch │ │ │ ├── Norm-stats-report-welch.pdf │ │ │ └── welch_stats.tsv │ ├── tiny_data.tsv │ ├── tiny_data_20rows.tsv │ ├── tiny_data_log2.tsv │ ├── tiny_data_no_annot.tsv │ ├── tiny_data_nonna.tsv │ ├── tiny_data_proteios.tsv │ ├── tiny_data_single_annot.tsv │ ├── tiny_design.tsv │ ├── tiny_design_singlecond.tsv │ └── tiny_design_singlerep.tsv └── testdata │ ├── anova.csv │ ├── calculateSummarizedCorrelationVector_pearson.csv │ └── calculateSummarizedCorrelationVector_spearman.csv ├── man ├── NormalyzerDataset.Rd ├── NormalyzerEvaluationResults.Rd ├── NormalyzerResults.Rd ├── NormalyzerStatistics.Rd ├── analyzeNormalizations.Rd ├── calculateANOVAPValues.Rd ├── calculateAvgMadMem.Rd ├── calculateAvgReplicateVariation.Rd ├── calculateContrasts.Rd ├── calculateCorrSum.Rd ├── calculateFeatureCV.Rd ├── calculatePercentageAvgDiffInMat.Rd ├── calculateReplicateCV.Rd ├── calculateSummarizedCorrelationVector.Rd ├── createDirectory.Rd ├── detectSingleReplicate.Rd ├── detectSingletonSample.Rd ├── elapsedSecondsBetweenSystimes.Rd ├── example_data.Rd ├── example_data_only_values.Rd ├── example_design.Rd ├── example_stat_data.Rd ├── example_stat_summarized_experiment.Rd ├── example_summarized_experiment.Rd ├── example_wide_data.Rd ├── example_wide_design.Rd ├── filterLowRep.Rd ├── findLowlyVariableFeaturesCVs.Rd ├── generateAnnotatedMatrix.Rd ├── generatePlots.Rd ├── generateStatsReport.Rd ├── getCombinedMatrix.Rd ├── getIndexList.Rd ├── getLowCountSampleFiltered.Rd ├── getRTNormalizedMatrix.Rd ├── getReplicateSortedData.Rd ├── getRowNAFilterContrast.Rd ├── getSmoothedRTNormalizedMatrix.Rd ├── getVerifiedNormalyzerObject.Rd ├── getWidenedRTRange.Rd ├── globalIntensityNormalization.Rd ├── loadData.Rd ├── loadDesign.Rd ├── loadRawDataFromFile.Rd ├── meanNormalization.Rd ├── medianNormalization.Rd ├── normMethods.Rd ├── normalyzer.Rd ├── normalyzerDE.Rd ├── performCyclicLoessNormalization.Rd ├── performGlobalRLRNormalization.Rd ├── performNoNormalization.Rd ├── performNormalizations.Rd ├── performQuantileNormalization.Rd ├── performSMADNormalization.Rd ├── performVSNNormalization.Rd ├── plotBoxPlot.Rd ├── plotCVvsIntensity.Rd ├── plotComparisonVenns.Rd ├── plotContrastPCA.Rd ├── plotContrastPHists.Rd ├── plotCorrelation.Rd ├── plotDendrograms.Rd ├── plotDensity.Rd ├── plotFrontPage.Rd ├── plotMA.Rd ├── plotMDS.Rd ├── plotMeanSD.Rd ├── plotPHist.Rd ├── plotQQ.Rd ├── plotRLE.Rd ├── plotReplicateVarAndStableVariables.Rd ├── plotReplicateVariance.Rd ├── plotSampleMappingPage.Rd ├── plotSampleOutlierSummary.Rd ├── plotScatter.Rd ├── plotSigScatter.Rd ├── preprocessData.Rd ├── printMeta.Rd ├── printPlots.Rd ├── reduceTechnicalReplicates.Rd ├── setupJobDir.Rd ├── setupPlotting.Rd ├── setupRawContrastObject.Rd ├── setupRawDataObject.Rd ├── setupTestData.Rd ├── validateSampleReplication.Rd ├── verifyContrasts.Rd ├── verifyDesignMatrix.Rd ├── verifyMultipleSamplesPresent.Rd ├── verifySummarizedExperiment.Rd ├── verifyValidNumbers.Rd └── writeNormalizedDatasets.Rd ├── tests ├── testthat.R └── testthat │ ├── test_analyzeResults.R │ ├── test_calculateStatistics.R │ ├── test_higherOrderNormMethods.R │ ├── test_inputVerification.R │ ├── test_normMethods.R │ ├── test_preparsers.R │ └── test_utils.R └── vignettes ├── 180813_normalyzerde_schematics.png └── vignette.Rmd /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComputationalProteomics/NormalyzerDE/HEAD/.gitignore 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