Files in ComputationalProteomics/NormalyzerDE
Evaluation of normalization methods and calculation of differential expression analysis statistics

.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/NormalyzerDE.R R/NormalyzerDataset.R R/NormalyzerEvaluationResults.R R/NormalyzerResults.R R/NormalyzerStatistics.R R/analyzeResults.R R/calculateStatistics.R R/data.R R/generatePlots.R R/higherOrderNormMethods.R R/inputVerification.R R/normMethods.R R/outputUtils.R R/preparsers.R R/printMeta.R R/printPlots.R R/utils.R README.md
data/example_data.rda
data/example_data_only_values.rda
data/example_data_only_values_small.rda
data/example_data_small.rda
data/example_design.rda
data/example_design_small.rda
data/example_stat_data.rda
data/example_stat_summarized_experiment.rda
data/example_summarized_experiment.rda
data/example_wide_data.rda
data/example_wide_design.rda
inst/CITATION
inst/extdata/data.tsv
inst/extdata/design.tsv
inst/extdata/design_tech_rep.tsv
inst/extdata/four_col_data.tsv
inst/extdata/four_col_design.tsv
inst/extdata/mq_peptides_100.txt
inst/extdata/mq_proteinGroups_100.txt
inst/extdata/stat_runs/batch/Norm-stats-report-batch.pdf
inst/extdata/stat_runs/batch/batch_stats.tsv
inst/extdata/stat_runs/log2/Norm-stats-report-log2.pdf
inst/extdata/stat_runs/log2/log2_stats.tsv
inst/extdata/stat_runs/multiple_comps/Norm-stats-report-multiple_comps.pdf
inst/extdata/stat_runs/multiple_comps/multiple_comps_stats.tsv
inst/extdata/stat_runs/normal/Norm-stats-report-unit_test_run_stat.pdf
inst/extdata/stat_runs/normal/normal_stats.tsv
inst/extdata/stat_runs/techrep/Norm-stats-report-techrep.pdf
inst/extdata/stat_runs/techrep/techrep_stats.tsv
inst/extdata/stat_runs/welch/Norm-stats-report-welch.pdf
inst/extdata/stat_runs/welch/welch_stats.tsv
inst/extdata/tiny_data.tsv
inst/extdata/tiny_data_20rows.tsv
inst/extdata/tiny_data_log2.tsv
inst/extdata/tiny_data_no_annot.tsv
inst/extdata/tiny_data_nonna.tsv
inst/extdata/tiny_data_proteios.tsv
inst/extdata/tiny_data_single_annot.tsv
inst/extdata/tiny_design.tsv
inst/extdata/tiny_design_singlecond.tsv
inst/extdata/tiny_design_singlerep.tsv
inst/testdata/anova.csv
inst/testdata/calculateSummarizedCorrelationVector_pearson.csv
inst/testdata/calculateSummarizedCorrelationVector_spearman.csv
man/NormalyzerDataset.Rd man/NormalyzerEvaluationResults.Rd man/NormalyzerResults.Rd man/NormalyzerStatistics.Rd man/analyzeNormalizations.Rd man/calculateANOVAPValues.Rd man/calculateAvgMadMem.Rd man/calculateAvgReplicateVariation.Rd man/calculateContrasts.Rd man/calculateCorrSum.Rd man/calculateFeatureCV.Rd man/calculatePercentageAvgDiffInMat.Rd man/calculateReplicateCV.Rd man/calculateSummarizedCorrelationVector.Rd man/createDirectory.Rd man/detectSingleReplicate.Rd man/detectSingletonSample.Rd man/elapsedSecondsBetweenSystimes.Rd man/example_data.Rd man/example_data_only_values.Rd man/example_design.Rd man/example_stat_data.Rd man/example_stat_summarized_experiment.Rd man/example_summarized_experiment.Rd man/example_wide_data.Rd man/example_wide_design.Rd man/filterLowRep.Rd man/findLowlyVariableFeaturesCVs.Rd man/generateAnnotatedMatrix.Rd man/generatePlots.Rd man/generateStatsReport.Rd man/getCombinedMatrix.Rd man/getIndexList.Rd man/getLowCountSampleFiltered.Rd man/getRTNormalizedMatrix.Rd man/getReplicateSortedData.Rd man/getRowNAFilterContrast.Rd man/getSmoothedRTNormalizedMatrix.Rd man/getVerifiedNormalyzerObject.Rd man/getWidenedRTRange.Rd man/globalIntensityNormalization.Rd man/loadData.Rd man/loadDesign.Rd man/loadRawDataFromFile.Rd man/meanNormalization.Rd man/medianNormalization.Rd man/normMethods.Rd man/normalyzer.Rd man/normalyzerDE.Rd man/performCyclicLoessNormalization.Rd man/performGlobalRLRNormalization.Rd man/performNoNormalization.Rd man/performNormalizations.Rd man/performQuantileNormalization.Rd man/performSMADNormalization.Rd man/performVSNNormalization.Rd man/plotBoxPlot.Rd man/plotCVvsIntensity.Rd man/plotComparisonVenns.Rd man/plotContrastPCA.Rd man/plotContrastPHists.Rd man/plotCorrelation.Rd man/plotDendrograms.Rd man/plotDensity.Rd man/plotFrontPage.Rd man/plotMA.Rd man/plotMDS.Rd man/plotMeanSD.Rd man/plotPHist.Rd man/plotQQ.Rd man/plotRLE.Rd man/plotReplicateVarAndStableVariables.Rd man/plotReplicateVariance.Rd man/plotSampleMappingPage.Rd man/plotSampleOutlierSummary.Rd man/plotScatter.Rd man/plotSigScatter.Rd man/preprocessData.Rd man/printMeta.Rd man/printPlots.Rd man/reduceTechnicalReplicates.Rd man/setupJobDir.Rd man/setupPlotting.Rd man/setupRawContrastObject.Rd man/setupRawDataObject.Rd man/setupTestData.Rd man/validateSampleReplication.Rd man/verifyContrasts.Rd man/verifyDesignMatrix.Rd man/verifyMultipleSamplesPresent.Rd man/verifySummarizedExperiment.Rd man/verifyValidNumbers.Rd man/writeNormalizedDatasets.Rd tests/testthat.R tests/testthat/test_analyzeResults.R tests/testthat/test_calculateStatistics.R tests/testthat/test_higherOrderNormMethods.R tests/testthat/test_inputVerification.R tests/testthat/test_normMethods.R
tests/testthat/test_preparsers.R
tests/testthat/test_utils.R
vignettes/180813_normalyzerde_schematics.png
vignettes/vignette.Rmd
ComputationalProteomics/NormalyzerDE documentation built on May 20, 2024, 3:05 p.m.