MANIFEST.in
README.rst
setup.cfg
setup.py
dreamtools/__init__.py
dreamtools.egg-info/PKG-INFO
dreamtools.egg-info/SOURCES.txt
dreamtools.egg-info/dependency_links.txt
dreamtools.egg-info/entry_points.txt
dreamtools.egg-info/not-zip-safe
dreamtools.egg-info/requires.txt
dreamtools.egg-info/top_level.txt
dreamtools/admin/__init__.py
dreamtools/admin/download_data.py
dreamtools/admin/mailing.py
dreamtools/admin/registered.py
dreamtools/core/__init__.py
dreamtools/core/challenge.py
dreamtools/core/cindex.py
dreamtools/core/downloader.py
dreamtools/core/layout.py
dreamtools/core/release.py
dreamtools/core/rocs.py
dreamtools/core/rtools.py
dreamtools/core/sageutils.py
dreamtools/core/scoring.py
dreamtools/core/settings.py
dreamtools/core/wikitools.py
dreamtools/core/ziptools.py
dreamtools/dream1/__init__.py
dreamtools/dream10/__init__.py
dreamtools/dream10/D10C1/__init__.py
dreamtools/dream10/D10C2/__init__.py
dreamtools/dream10/D10C3/__init__.py
dreamtools/dream2/__init__.py
dreamtools/dream2/D2C1/__init__.py
dreamtools/dream2/D2C1/scoring.py
dreamtools/dream2/D2C1/data/BCL6_targets_and_decoys.xls
dreamtools/dream2/D2C1/data/FromNumbersToGeneNames.txt
dreamtools/dream2/D2C1/data/__init__.py
dreamtools/dream2/D2C1/data/__init__.pyc
dreamtools/dream2/D2C1/goldstandard/D2C1_goldstandard.tsv
dreamtools/dream2/D2C1/goldstandard/GoldStandard_with_AffyIds.xls
dreamtools/dream2/D2C1/goldstandard/__init__.py
dreamtools/dream2/D2C1/templates/D2C1_template.tsv
dreamtools/dream2/D2C1/templates/__init__.py
dreamtools/dream2/D2C2/__init__.py
dreamtools/dream2/D2C2/scoring.py
dreamtools/dream2/D2C2/data/FromNumbersToGeneNames.txt
dreamtools/dream2/D2C2/data/INFO.txt
dreamtools/dream2/D2C2/data/Prot-Prot_Genes.xls
dreamtools/dream2/D2C2/goldstandard/D2C2_goldstandard.txt
dreamtools/dream2/D2C2/goldstandard/GoldStandard_ProtProtSubnet.txt
dreamtools/dream2/D2C2/templates/D2C2_template.txt
dreamtools/dream2/D2C3/__init__.py
dreamtools/dream2/D2C3/scoring.py
dreamtools/dream2/D2C3/data/FiveGene_chip.xls
dreamtools/dream2/D2C3/data/FiveGene_qPCR.xls
dreamtools/dream2/D2C3/data/INFO.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_DIRECTED-SIGNED_EXCITATORY_chip.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_DIRECTED-SIGNED_EXCITATORY_qPCR.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_DIRECTED-SIGNED_INHIBITORY_chip.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_DIRECTED-SIGNED_INHIBITORY_qPCR.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_DIRECTED-UNSIGNED_chip.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_DIRECTED-UNSIGNED_qPCR.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_UNDIRECTED-SIGNED_EXCITATORY_chip.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_UNDIRECTED-SIGNED_EXCITATORY_qPCR.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_UNDIRECTED-SIGNED_INHIBITORY_chip.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_UNDIRECTED-SIGNED_INHIBITORY_qPCR.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_UNDIRECTED-UNSIGNED_chip.txt
dreamtools/dream2/D2C3/goldstandard/D2C3_goldstandard_UNDIRECTED-UNSIGNED_qPCR.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_DIRECTED-SIGNED_EXCITATORY_chip.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_DIRECTED-SIGNED_EXCITATORY_qPCR.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_DIRECTED-SIGNED_INHIBITORY_chip.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_DIRECTED-SIGNED_INHIBITORY_qPCR.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_DIRECTED-UNSIGNED_chip.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_DIRECTED-UNSIGNED_qPCR.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_UNDIRECTED-SIGNED_EXCITATORY_chip.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_UNDIRECTED-SIGNED_EXCITATORY_qPCR.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_UNDIRECTED-SIGNED_INHIBITORY_chip.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_UNDIRECTED-SIGNED_INHIBITORY_qPCR.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_UNDIRECTED-UNSIGNED_chip.txt
dreamtools/dream2/D2C3/templates/D2C3_templates_UNDIRECTED-UNSIGNED_qPCR.txt
dreamtools/dream2/D2C4/__init__.py
dreamtools/dream2/D2C4/scoring.py
dreamtools/dream2/D2C5/__init__.py
dreamtools/dream2/D2C5/scoring.py
dreamtools/dream3/__init__.py
dreamtools/dream3/D3C1/__init__.py
dreamtools/dream3/D3C1/scoring.py
dreamtools/dream3/D3C1/goldstandard/D3C1_goldstandard.txt
dreamtools/dream3/D3C1/templates/D3C1_template.txt
dreamtools/dream3/D3C2/__init__.py
dreamtools/dream3/D3C2/scoring.py
dreamtools/dream3/D3C2/goldstandard/D3C2_goldstandard_cytokine.txt
dreamtools/dream3/D3C2/goldstandard/D3C2_goldstandard_phospho.txt
dreamtools/dream3/D3C2/templates/D3C2_template_cytokine.txt
dreamtools/dream3/D3C2/templates/D3C2_template_phospho.txt
dreamtools/dream3/D3C3/__init__.py
dreamtools/dream3/D3C3/scoring.py
dreamtools/dream3/D3C3/goldstandard/D3C3_goldstandard.txt
dreamtools/dream3/D3C3/templates/D3C3_template.txt
dreamtools/dream3/D3C4/__init__.py
dreamtools/dream3/D3C4/scoring.py
dreamtools/dream3/D3C4/templates/example_InSilicoSize10_Ecoli1.txt
dreamtools/dream3/D3C4/templates/example_InSilicoSize10_Ecoli2.txt
dreamtools/dream3/D3C4/templates/example_InSilicoSize10_Yeast1.txt
dreamtools/dream3/D3C4/templates/example_InSilicoSize10_Yeast2.txt
dreamtools/dream3/D3C4/templates/example_InSilicoSize10_Yeast3.txt
dreamtools/dream4/__init__.py
dreamtools/dream4/D4C1/__init__.py
dreamtools/dream4/D4C1/scoring.py
dreamtools/dream4/D4C1/goldstandard/D4C1_goldstandard.txt
dreamtools/dream4/D4C1/goldstandard/README.rst
dreamtools/dream4/D4C1/templates/D4C1_templates.txt
dreamtools/dream4/D4C2/__init__.py
dreamtools/dream4/D4C2/scoring.py
dreamtools/dream4/D4C2/goldstandard/10/DREAM4_GoldStandard_InSilico_Size10_1.tsv
dreamtools/dream4/D4C2/goldstandard/10/DREAM4_GoldStandard_InSilico_Size10_2.tsv
dreamtools/dream4/D4C2/goldstandard/10/DREAM4_GoldStandard_InSilico_Size10_3.tsv
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dreamtools/dream4/D4C2/goldstandard/10/DREAM4_GoldStandard_InSilico_Size10_5.tsv
dreamtools/dream4/D4C2/goldstandard/100/DREAM4_GoldStandard_InSilico_Size100_1.tsv
dreamtools/dream4/D4C2/goldstandard/100/DREAM4_GoldStandard_InSilico_Size100_2.tsv
dreamtools/dream4/D4C2/goldstandard/100/DREAM4_GoldStandard_InSilico_Size100_3.tsv
dreamtools/dream4/D4C2/goldstandard/100/DREAM4_GoldStandard_InSilico_Size100_4.tsv
dreamtools/dream4/D4C2/goldstandard/100/DREAM4_GoldStandard_InSilico_Size100_5.tsv
dreamtools/dream4/D4C2/goldstandard/100_multifactorial/DREAM4_GoldStandard_InSilico_Size100_multifactorial_1.tsv
dreamtools/dream4/D4C2/goldstandard/100_multifactorial/DREAM4_GoldStandard_InSilico_Size100_multifactorial_2.tsv
dreamtools/dream4/D4C2/goldstandard/100_multifactorial/DREAM4_GoldStandard_InSilico_Size100_multifactorial_3.tsv
dreamtools/dream4/D4C2/goldstandard/100_multifactorial/DREAM4_GoldStandard_InSilico_Size100_multifactorial_4.tsv
dreamtools/dream4/D4C2/goldstandard/100_multifactorial/DREAM4_GoldStandard_InSilico_Size100_multifactorial_5.tsv
dreamtools/dream4/D4C2/templates/10/DREAM4_Example_InSilico_Size10_1.txt
dreamtools/dream4/D4C2/templates/10/DREAM4_Example_InSilico_Size10_2.txt
dreamtools/dream4/D4C2/templates/10/DREAM4_Example_InSilico_Size10_3.txt
dreamtools/dream4/D4C2/templates/10/DREAM4_Example_InSilico_Size10_4.txt
dreamtools/dream4/D4C2/templates/10/DREAM4_Example_InSilico_Size10_5.txt
dreamtools/dream4/D4C2/templates/100/DREAM4_Example_InSilico_Size100_1.txt
dreamtools/dream4/D4C2/templates/100/DREAM4_Example_InSilico_Size100_2.txt
dreamtools/dream4/D4C2/templates/100/DREAM4_Example_InSilico_Size100_3.txt
dreamtools/dream4/D4C2/templates/100/DREAM4_Example_InSilico_Size100_4.txt
dreamtools/dream4/D4C2/templates/100/DREAM4_Example_InSilico_Size100_5.txt
dreamtools/dream4/D4C2/templates/100_multifactorial/DREAM4_Example_InSilico_Size100_multifactorial_1.txt
dreamtools/dream4/D4C2/templates/100_multifactorial/DREAM4_Example_InSilico_Size100_multifactorial_2.txt
dreamtools/dream4/D4C2/templates/100_multifactorial/DREAM4_Example_InSilico_Size100_multifactorial_3.txt
dreamtools/dream4/D4C2/templates/100_multifactorial/DREAM4_Example_InSilico_Size100_multifactorial_4.txt
dreamtools/dream4/D4C2/templates/100_multifactorial/DREAM4_Example_InSilico_Size100_multifactorial_5.txt
dreamtools/dream4/D4C3/__init__.py
dreamtools/dream4/D4C3/scoring.py
dreamtools/dream4/D4C3/data/common_gold.csv
dreamtools/dream4/D4C3/data/common_training.csv
dreamtools/dream4/D4C3/data/pdf_score_1.mat
dreamtools/dream4/D4C3/data/pdf_score_2.mat
dreamtools/dream4/D4C3/data/pdf_score_3.mat
dreamtools/dream4/D4C3/data/pdf_score_4.mat
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dreamtools/dream4/D4C3/data/pdf_score_6.mat
dreamtools/dream4/D4C3/data/pdf_score_7.mat
dreamtools/dream4/D4C3/goldstandard/D4C3_goldstandard.csv
dreamtools/dream4/D4C3/templates/D4C3_templates.csv
dreamtools/dream5/__init__.py
dreamtools/dream5/D5C1/__init__.py
dreamtools/dream5/D5C1/scoring.py
dreamtools/dream5/D5C1/data/DREAM5_EAR_TestSet.txt
dreamtools/dream5/D5C1/data/DREAM5_EAR_TrainingSet.txt
dreamtools/dream5/D5C2/__init__.py
dreamtools/dream5/D5C2/scoring.py
dreamtools/dream5/D5C2/data/d5c2_data_plot.csv
dreamtools/dream5/D5C2/data/d5c2_data_table.csv
dreamtools/dream5/D5C3/__init__.py
dreamtools/dream5/D5C3/scoring.py
dreamtools/dream5/D5C3/data/DREAM5_SysGenB_Predictions.csv
dreamtools/dream5/D5C3/goldstandard/DREAM5_SysGenB1_TestPhenotypeData.txt
dreamtools/dream5/D5C3/goldstandard/DREAM5_SysGenB2_TestPhenotypeData.txt
dreamtools/dream5/D5C3/goldstandard/DREAM5_SysGenB3_TestPhenotypeData.txt
dreamtools/dream5/D5C3/templates/DREAM5_SysGenB1_your_Predictions.txt
dreamtools/dream5/D5C3/templates/DREAM5_SysGenB2_your_Predictions.txt
dreamtools/dream5/D5C3/templates/DREAM5_SysGenB3_your_Predictions.txt
dreamtools/dream5/D5C4/__init__.py
dreamtools/dream5/D5C4/scoring.py
dreamtools/dream6/__init__.py
dreamtools/dream6/D6C1/__init__.py
dreamtools/dream6/D6C1/scoring.py
dreamtools/dream6/D6C1/leaderboards/LB.csv
dreamtools/dream6/D6C2/__init__.py
dreamtools/dream6/D6C2/scoring.py
dreamtools/dream6/D6C3/__init__.py
dreamtools/dream6/D6C3/scoring.py
dreamtools/dream6/D6C3/data/D6C3_data.zip
dreamtools/dream6/D6C3/data/predictions/Dream6_expred_predictions_BioFeatures+FiRST.txt
dreamtools/dream6/D6C3/data/predictions/dream6_expred_predictions_10.txt
dreamtools/dream6/D6C3/data/predictions/dream6_expred_predictions_11.txt
dreamtools/dream6/D6C3/data/predictions/dream6_expred_predictions_12.txt
dreamtools/dream6/D6C3/data/predictions/dream6_expred_predictions_13.txt
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dreamtools/dream6/D6C3/data/predictions/dream6_expred_predictions_15.txt
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dreamtools/dream6/D6C3/data/predictions/dream6_expred_predictions_FiRST.txt
dreamtools/dream6/D6C3/data/predictions/dream6_expred_predictions_c4lab.txt
dreamtools/dream6/D6C3/goldstandard/D6C3_goldstandard.txt
dreamtools/dream6/D6C3/templates/D6C3_template.txt
dreamtools/dream6/D6C3/templates/Supplemental_Material.zip
dreamtools/dream6/D6C3/templates/DREAM6_Predictions/Dream6_expred_predictions_BioFeatures+FiRST.txt
dreamtools/dream6/D6C3/templates/DREAM6_Predictions/dream6_expred_predictions_10.txt
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dreamtools/dream6/D6C3/templates/DREAM6_Predictions/dream6_expred_predictions_9.txt
dreamtools/dream6/D6C3/templates/DREAM6_Predictions/dream6_expred_predictions_FiRST.txt
dreamtools/dream6/D6C3/templates/DREAM6_Predictions/dream6_expred_predictions_c4lab.txt
dreamtools/dream6/D6C4/__init__.py
dreamtools/dream6/D6C4/scoring.py
dreamtools/dream6/D6C4/data/AMLTraining.csv
dreamtools/dream6/D6C4/data/DREAM6_AML_FilesTubesAndSubjects.CSV
dreamtools/dream6/D6C4/data/DREAM6_AML_TrainingSet.csv
dreamtools/dream6/D6C4/data/DREAM6_flowcap_download_info.txt
dreamtools/dream6/D6C4/goldstandard/AML.csv
dreamtools/dream6/D6C4/goldstandard/D6C4_goldstandard.txt
dreamtools/dream6/D6C4/misc/AML.R
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dreamtools/dream6/data/__init__.py
dreamtools/dream6/parest/__init__.py
dreamtools/dream6/parest/dream6_challenge2.py
dreamtools/dream7/__init__.py
dreamtools/dream7/D7C1/__init__.py
dreamtools/dream7/D7C1/scoring.py
dreamtools/dream7/D7C1/data/D7C1_param_proba.npy
dreamtools/dream7/D7C1/goldstandard/model1_parameters_answer.txt
dreamtools/dream7/D7C1/goldstandard/model1_prediction_answer.txt
dreamtools/dream7/D7C1/goldstandard/model2_parameters_answer.txt
dreamtools/dream7/D7C1/goldstandard/model2_topology_answer.txt
dreamtools/dream7/D7C1/templates/model1_parameters_alphabeta.txt
dreamtools/dream7/D7C1/templates/model1_timecourse_alphabeta.txt
dreamtools/dream7/D7C1/templates/model2_parameters_alphabeta.txt
dreamtools/dream7/D7C1/templates/network_topology_alphabeta.txt
dreamtools/dream7/D7C2/__init__.py
dreamtools/dream7/D7C2/scoring.py
dreamtools/dream7/D7C2/BCC/R/DemoModel.R
dreamtools/dream7/D7C2/BCC/R/evaluateMetabricModelFromCode.R
dreamtools/dream7/D7C2/BCC/R/loadMetabricTestData.R
dreamtools/dream7/D7C2/BCC/R/loadMetabricTestData_federation.R
dreamtools/dream7/D7C2/BCC/R/loadMetabricTrainingData.R
dreamtools/dream7/D7C2/BCC/R/loadMetabricTrainingData_federation.R
dreamtools/dream7/D7C2/BCC/R/restoreSessionAndCreateNewModelFromOSModel.R
dreamtools/dream7/D7C2/BCC/R/retrainAllOSModels.R
dreamtools/dream7/D7C2/BCC/R/retrainOSModel.R
dreamtools/dream7/D7C2/BCC/R/submitCompetitionModel.R
dreamtools/dream7/D7C2/BCC/inst/metabricCompetitionDemo.R
dreamtools/dream7/D7C2/BCC/inst/metabricCompetitionDemo_diseaseSpecificSurvival.R
dreamtools/dream7/D7C2/data/README.rst
dreamtools/dream7/D7C2/misc/exactConcordanceIndex.R
dreamtools/dream7/D7C2/misc/exactConcordanceIndexV.R
dreamtools/dream7/D7C2/predictiveModeling/R/CaretModel.R
dreamtools/dream7/D7C2/predictiveModeling/R/CoxModel.R
dreamtools/dream7/D7C2/predictiveModeling/R/GlmnetModel.R
dreamtools/dream7/D7C2/predictiveModeling/R/LinearModel.R
dreamtools/dream7/D7C2/predictiveModeling/R/MostCorrelatedFeatures.R
dreamtools/dream7/D7C2/predictiveModeling/R/PredictiveModel.R
dreamtools/dream7/D7C2/predictiveModeling/R/PredictiveModelFeatureEvaluator.R
dreamtools/dream7/D7C2/predictiveModeling/R/PredictiveModelPerformance.R
dreamtools/dream7/D7C2/predictiveModeling/R/PredictiveModelResults.R
dreamtools/dream7/D7C2/predictiveModeling/R/RSFmodel.R
dreamtools/dream7/D7C2/predictiveModeling/R/SurvivalModelPerformance.R
dreamtools/dream7/D7C2/predictiveModeling/R/SurvivalModelPerformanceCV.R
dreamtools/dream7/D7C2/predictiveModeling/R/convertDataFrameToFeatureMatrix.R
dreamtools/dream7/D7C2/predictiveModeling/R/createAggregateFeatureDataSet.R
dreamtools/dream7/D7C2/predictiveModeling/R/createENetTuneGrid.R
dreamtools/dream7/D7C2/predictiveModeling/R/createFeatureAndResponseDataList.R
dreamtools/dream7/D7C2/predictiveModeling/R/crossValidatePredictiveModel.R
dreamtools/dream7/D7C2/predictiveModeling/R/crossValidatePredictiveSurvivalModel.R
dreamtools/dream7/D7C2/predictiveModeling/R/defaultTrainControl.R
dreamtools/dream7/D7C2/predictiveModeling/R/exactConcordanceIndex.R
dreamtools/dream7/D7C2/predictiveModeling/R/exactConcordanceIndexV.R
dreamtools/dream7/D7C2/predictiveModeling/R/filterNasFromMatrix.R
dreamtools/dream7/D7C2/predictiveModeling/R/filterPredictiveModelData.R
dreamtools/dream7/D7C2/predictiveModeling/R/jet.colors.R
dreamtools/dream7/D7C2/predictiveModeling/R/plotPredictiveModelHeatmap.R
dreamtools/dream7/D7C2/predictiveModeling/R/testPackage.R
dreamtools/dream7/D7C2/predictiveModeling/R/trainPartition.R
dreamtools/dream7/D7C2/predictiveModeling/R/zzz.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/Anova.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/Boot.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/Boxplot.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/Contrasts.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/Ellipse.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/TransformationAxes.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/avPlots.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/bootCase.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/boxCox.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/boxCoxVariable.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/boxTidwell.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/car-deprecated.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/carWeb.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/ceresPlots.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/compareCoefs.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/crPlots.R
dreamtools/dream7/D7C2/predictiveModeling/car/R/deltaMethod.R
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