Files in TReNA
Fit transcriptional regulatory networks using gene expression, priors, machine learning
DESCRIPTION
_config.yml
README.md
NAMESPACE
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
build/vignette.rds
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/NEWS
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/extdata/all_motifs.meme
inst/extdata/ampAD.154genes.mef2cTFs.278samples.RData
inst/extdata/ampAD.58genes.mef2cTFs.278samples.RData
inst/extdata/yeast-53genes-536-samples.RData
inst/extdata/project.sub.db
inst/extdata/genome.sub.db
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/misc/footprintFinding/piq/makefile
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.html
inst/doc/TReNA_Vignette.Rmd
inst/notes/fillEnhancerDatabase.txt
inst/demos/findTFs.R
inst/demos/demoEnhancersDatabaseOnWhovian.R
inst/demos/findPiez02RegulatorySnps.R
inst/demos/test.png
inst/demos/runLassoSolver.R
inst/demos/Assess_Distributions.ipynb
inst/demos/trem2/go.R
