Files in TReNA

Fit transcriptional regulatory networks using gene expression, priors, machine learning

README.md vignettes/TReNA_Vignette.Rmd man/LassoPVSolver-class.Rd man/EnsembleSolver-class.Rd man/VarianceFilter-class.Rd man/getAssayData.Rd man/getGtfMoleculeTypes.Rd man/RidgeSolver-class.Rd man/getGenePromoterRegion.Rd man/NullFilter-class.Rd man/RandomForestSolver-class.Rd man/solve.LassoPV.Rd man/TReNA-class.Rd man/solve.Ridge.Rd man/LassoSolver.Rd man/TReNA-package.Rd man/getCandidates-FootprintFilter-method.Rd man/rescalePredictorWeights.Rd man/solve.Pearson.Rd man/SqrtLassoSolver-class.Rd man/getFootprintsInRegion.Rd man/getPromoterRegionsAllGenes.Rd man/getGtfGeneBioTypes.Rd man/FootprintFilter-class.Rd man/solve.Rd man/PearsonSolver.Rd man/solve.RandomForest.Rd man/BayesSpikeSolver-class.Rd man/LassoPVSolver.Rd man/getFilterAssayData.Rd man/getChromLoc.Rd man/solve.SqrtLasso.Rd man/solve.Ensemble.Rd man/RidgeSolver.Rd man/getSolverName.Rd man/solve.BayesSpike.Rd man/getCandidates.Rd man/PearsonSolver-class.Rd man/FootprintFinder-class.Rd man/EnsembleSolver.Rd man/Solver-class.Rd man/RandomForestSolver.Rd man/closeDatabaseConnections.Rd man/SpearmanSolver.Rd man/CandidateFilter-class.Rd man/SpearmanSolver-class.Rd man/SqrtLassoSolver.Rd man/mapMotifsToTFsMergeIntoTable.Rd man/getCandidates-VarianceFilter-method.Rd man/solve.Spearman.Rd man/solve.Lasso.Rd man/LassoSolver-class.Rd man/BayesSpikeSolver.Rd man/getSolverObject.Rd man/getCandidates-NullFilter-method.Rd man/getFootprintsForGene.Rd tests/runTests.R R/CandidateFilter.R R/RidgeSolver.R R/help.R R/PearsonSolver.R R/NullFilter.R R/SqrtLassoSolver.R R/LassoSolver.R R/BayesSpikeSolver.R R/LassoPVSolver.R R/Solver.R R/sharedFunctions.R R/VarianceFilter.R R/FootprintFinder.R R/RandomForestSolver.R R/EnsembleSolver.R R/FootprintFilter.R R/SpearmanSolver.R R/TReNA.R inst/prep/dream5.yeast/createTestData.R inst/utils/evaluateAllSolvers.R inst/utils/createGenomeScaleModel.R inst/utils/test_runTReNA.R inst/utils/determineSqrtLambda.R inst/utils/extraFunctions.R inst/utils/additionalTReNATests.R inst/utils/runTReNA.R inst/misc/runTReNA-demo.R inst/misc/createSQLiteDB.R inst/misc/makeTRN-proximalonly-demo.R inst/misc/makeTRN-proximalanddistal-demo.R inst/misc/monteCarloTRN.R inst/unitTests/test_SpearmanSolver.R inst/unitTests/test_EnsembleSolver.R inst/unitTests/test_FootprintFinder.R inst/unitTests/test_Solver.R inst/unitTests/test_LassoSolver.R inst/unitTests/test_TReNA.R inst/unitTests/test_VarianceFilter.R inst/unitTests/test_FootprintFilter.R inst/unitTests/test_RidgeSolver.R inst/unitTests/test_BayesSpikeSolver.R inst/unitTests/test_CandidateFilter.R inst/unitTests/test_SqrtLassoSolver.R inst/unitTests/test_PearsonSolver.R inst/unitTests/test_LassoPVSolver.R inst/unitTests/test_NullFilter.R inst/unitTests/test_RandomForestSolver.R inst/doc/TReNA_Vignette.R inst/doc/TReNA_Vignette.Rmd inst/demos/findTFs.R inst/demos/demoEnhancersDatabaseOnWhovian.R inst/demos/findPiez02RegulatorySnps.R inst/demos/runLassoSolver.R inst/demos/trem2/go.R