├── .github └── workflows │ └── maven.yml ├── .gitignore ├── LICENSE ├── README.md ├── Tests ├── DummyChangeDetector.java └── ProteomicsLoaderTest.java ├── pom.xml ├── src └── main │ └── java │ └── org │ └── panda │ └── causalpath │ ├── analyzer │ ├── CausalityHelper.java │ ├── CausalitySearcher.java │ ├── ComparisonDetector.java │ ├── CorrelationDetector.java │ ├── DataLabelShuffler.java │ ├── DataLabelShufflerForCorrelation.java │ ├── DifferenceDetector.java │ ├── DownstreamCounterForComparison.java │ ├── DownstreamCounterForCorrelation.java │ ├── EmpiricalPValueCalculator.java │ ├── FDRAdjuster.java │ ├── FDRAdjusterForCorrelation.java │ ├── FoldChangeDetector.java │ ├── KinaseActivityAnalyzer.java │ ├── LibraryPValueCalculator.java │ ├── NSCForComparison.java │ ├── NSCForCorrelation.java │ ├── NetworkSignificanceCalculator.java │ ├── OneDataChangeDetector.java │ ├── PValueCalculator.java │ ├── PropagationAccuracyPredictor.java │ ├── RobustnessAnalysis.java │ ├── SignificanceDetector.java │ ├── SignificanceDetectorWithSignedPValues.java │ ├── ThresholdDetector.java │ └── TwoDataChangeDetector.java │ ├── data │ ├── Activity.java │ ├── ActivityData.java │ ├── ActivityOfTFData.java │ ├── CNA.java │ ├── CNAData.java │ ├── CategoricalData.java │ ├── DataType.java │ ├── ExperimentData.java │ ├── GeneWithData.java │ ├── MetaboliteData.java │ ├── MethylationData.java │ ├── Mutation.java │ ├── MutationData.java │ ├── NumericData.java │ ├── Presence.java │ ├── PresenceData.java │ ├── ProteinData.java │ ├── ProteinSite.java │ ├── RNAData.java │ ├── SingleCategoricalData.java │ └── SiteModProteinData.java │ ├── network │ ├── GraphFilter.java │ ├── GraphWriter.java │ ├── Relation.java │ └── RelationType.java │ ├── resource │ ├── NetworkLoader.java │ ├── ProteomicsFileReader.java │ ├── ProteomicsLoader.java │ ├── RNALoader.java │ └── TCGALoader.java │ └── run │ ├── CausalPath.java │ ├── CausalityAnalysisSingleMethodInterface.java │ ├── JasonizeResultGraphsRecursively.java │ ├── MergeResultsIntoSeriesView.java │ ├── PrepareBoxPlots.java │ ├── ReportDifferentiallyExpressed.java │ ├── RunRecursive.java │ ├── TCGAEffectOfMutationRun.java │ ├── TCGARecurrentCorrelationRun.java │ └── ViewNeighborhoodInPriors.java └── wiki ├── EGF-stimulation-time-series.gif ├── InputFormat.md ├── OutputFiles.md ├── gpvi_mass_spec ├── 1-s2.0-S0006497120799349-mmc2.xlsx ├── causative.format ├── causative.json ├── causative.sif ├── conflicting.format ├── conflicting.json ├── conflicting.sif ├── data_causalpath.txt ├── parameters.txt ├── phospho_mass_spec_data_extract.R ├── results.txt ├── significance-pvals.txt ├── unknown-site-effects.txt └── value-changes.txt ├── rtutorial ├── causalpath.Rmd ├── causalpath.md ├── causalpath_files │ └── figure-markdown_github │ │ ├── unnamed-chunk-5-1.png │ │ └── unnamed-chunk-7-1.png └── dataset │ ├── data-fdr0.1.txt │ └── parameters.txt ├── sample-data-and-parameters.zip ├── sample.png └── sample.svg 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