Files in PriceLab/trena-until-01mar2018

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

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/BayesSpikeSolver.R R/CandidateFilter.R R/EnsembleSolver.R R/FootprintFilter.R R/FootprintFinder.R R/GeneOntologyFilter.R R/HumanDHSFilter.R R/LassoPVSolver.R R/LassoSolver.R R/MotifMatcher.R R/PearsonSolver.R R/RandomForestSolver.R R/RidgeSolver.R R/Solver.R R/SpearmanSolver.R R/SqrtLassoSolver.R R/Trena.R R/VarianceFilter.R R/help.R R/sharedFunctions.R R/utils.R README.md

_config.yml

inst/.DS_Store

inst/NEWS

inst/demos/.DS_Store

inst/demos/Assess_Distributions.ipynb

inst/demos/demoEnhancersDatabaseOnWhovian.R inst/demos/findPiez02RegulatorySnps.R inst/demos/findTFs.R inst/demos/runLassoSolver.R

inst/demos/test.png

inst/demos/trem2/go.R

inst/extdata/all_motifs.meme

inst/extdata/ampAD.154genes.mef2cTFs.278samples.RData

inst/extdata/ampAD.58genes.mef2cTFs.278samples.RData

inst/extdata/human.regulatory.genes.RData

inst/extdata/mef2c.neigborhood.hg38.footprints.db

inst/extdata/mef2c.neighborhood.hg38.gtfAnnotation.db

inst/extdata/motifGenes.tsv

inst/extdata/vrk2.neigborhood.hg38.footprints.db

inst/extdata/vrk2.neighborhood.hg38.gtfAnnotation.db

inst/extdata/yeast-53genes-536-samples.RData

inst/misc/.DS_Store

inst/misc/assessSnp.R inst/misc/createSQLiteDB.R

inst/misc/footprintFinding/piq/makefile

inst/misc/makeTRN-proximalanddistal-demo.R inst/misc/makeTRN-proximalonly-demo.R inst/misc/monteCarloTRN.R inst/misc/multiModels/aqp4-multi.R inst/misc/multiModels/aqp4.R inst/misc/multiModels/graphToJSON-devel.R

inst/misc/multiModels/style.js

inst/misc/profileDbQueries.R inst/misc/runTReNA-demo.R

inst/notes/fillEnhancerDatabase.txt

inst/prep/dream5.yeast/createTestData.R

inst/prep/dream5.yeast/net4_expression_data.tsv

inst/prep/dream5.yeast/net4_gene_ids.tsv

inst/prep/dream5.yeast/net4_transcription_factors.tsv

inst/prep/dream5.yeast/yeastGoldStandard.tsv

inst/unitTests/bugDemo001.R inst/unitTests/test_BayesSpikeSolver.R inst/unitTests/test_CandidateFilter.R inst/unitTests/test_EnsembleSolver.R inst/unitTests/test_FootprintFilter.R inst/unitTests/test_FootprintFinder.R inst/unitTests/test_GeneOntologyFilter.R inst/unitTests/test_HumanDHSFilter.R inst/unitTests/test_LassoPVSolver.R inst/unitTests/test_LassoSolver.R inst/unitTests/test_MotifMatcher.R inst/unitTests/test_PearsonSolver.R inst/unitTests/test_RandomForestSolver.R inst/unitTests/test_RidgeSolver.R inst/unitTests/test_Solver.R inst/unitTests/test_SpearmanSolver.R inst/unitTests/test_SqrtLassoSolver.R inst/unitTests/test_Trena.R inst/unitTests/test_VarianceFilter.R inst/utils/NaiveSolver.R inst/utils/TReNA.R inst/utils/additionalTReNATests.R inst/utils/createGenomeScaleModel.R inst/utils/createGlobusTable.R

inst/utils/currentDBs.html

inst/utils/determineSqrtLambda.R inst/utils/evaluateAllSolvers.R inst/utils/extraFunctions.R inst/utils/runTReNA.R inst/utils/test_NaiveSolver.R inst/utils/test_TReNA.R inst/utils/test_runTReNA.R

man/.DS_Store

man/BayesSpikeSolver-class.Rd man/BayesSpikeSolver.Rd man/CandidateFilter-class.Rd man/EnsembleSolver-class.Rd man/EnsembleSolver.Rd man/FootprintFilter-class.Rd man/FootprintFinder-class.Rd man/GeneOntologyFilter-class.Rd man/HumanDHSFilter-class.Rd man/LassoPVSolver-class.Rd man/LassoPVSolver.Rd man/LassoSolver-class.Rd man/LassoSolver.Rd man/MotifMatcher-class.Rd man/PearsonSolver-class.Rd man/PearsonSolver.Rd man/RandomForestSolver-class.Rd man/RandomForestSolver.Rd man/RidgeSolver-class.Rd man/RidgeSolver.Rd man/Solver-class.Rd man/SpearmanSolver-class.Rd man/SpearmanSolver.Rd man/SqrtLassoSolver-class.Rd man/SqrtLassoSolver.Rd man/TReNA-package.Rd man/Trena-class.Rd man/VarianceFilter-class.Rd man/assessSnp.Rd man/closeDatabaseConnections.Rd man/createGeneModel.Rd man/findMatchesByChromosomalRegion.Rd man/getAssayData.Rd man/getAvailableSolvers.Rd man/getCandidates-FootprintFilter-method.Rd man/getCandidates-GeneOntologyFilter-method.Rd man/getCandidates-HumanDHSFilter-method.Rd man/getCandidates-VarianceFilter-method.Rd man/getCandidates.Rd man/getChromLoc.Rd man/getEncodeRegulatoryTableNames-HumanDHSFilter.Rd man/getFootprintsForGene.Rd man/getFootprintsInRegion.Rd man/getGeneModelTableColumnNames.Rd man/getGenePromoterRegion.Rd man/getGtfGeneBioTypes.Rd man/getGtfMoleculeTypes.Rd man/getPfms.Rd man/getPromoterRegionsAllGenes.Rd man/getProximalPromoter.Rd man/getRegulators.Rd man/getRegulatoryChromosomalRegions.Rd man/getRegulatoryRegions.Rd man/getRegulatoryTableColumnNames.Rd man/getSequence.Rd man/getSolverNames.Rd man/getTarget.Rd man/parseChromLocString.Rd man/parseDatabaseUri.Rd man/rescalePredictorWeights.Rd man/run.Rd man/show-HumanDHSFilter-method.Rd man/show.BayesSpikeSolver.Rd man/show.EnsembleSolver.Rd man/show.LassoPVSolver.Rd man/show.LassoSolver.Rd man/show.MotifMatcher.Rd man/show.PearsonSolver.Rd man/show.RandomForestSolver.Rd man/show.RidgeSolver.Rd man/show.SpearmanSolver.Rd man/show.SqrtLassoSolver.Rd man/solve.BayesSpike.Rd man/solve.Ensemble.Rd man/solve.Lasso.Rd man/solve.LassoPV.Rd man/solve.Pearson.Rd man/solve.RandomForest.Rd man/solve.Ridge.Rd man/solve.Spearman.Rd man/solve.SqrtLasso.Rd tests/runTests.R vignettes/TReNA_Vignette.Rmd

vignettes/TReNA_Vignette.html

PriceLab/trena-until-01mar2018 documentation built on May 25, 2019, 1:22 p.m.