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
