Files in PriceLab/TReNA
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/PCAMax.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/XGBoostSolver.R R/help.R R/sharedFunctions.R R/utils.R README.md
_config.yml
build.makefile
docs/404.html
docs/articles/TReNA_Vignette.html
docs/articles/TReNA_Vignette_files/figure-html/unnamed-chunk-3-1.png
docs/articles/TReNA_Vignette_files/figure-html/unnamed-chunk-5-1.png
docs/articles/caseStudyFour.html
docs/articles/caseStudyOne.html
docs/articles/caseStudyThree.html
docs/articles/caseStudyTwo.html
docs/articles/igvR-nfe2-regulation-noGeneHancer.png
docs/articles/igvR-nfe2-regulation.png
docs/articles/index.html
docs/articles/nfe2-regulation-old.html
docs/articles/overview.html
docs/articles/simple.html
docs/articles/simple_files/figure-html/unnamed-chunk-2-1.png
docs/articles/simple_files/figure-html/unnamed-chunk-2-2.png
docs/articles/tiny.html
docs/articles/tiny_files/figure-html/unnamed-chunk-2-1.png
docs/articles/tiny_files/figure-html/unnamed-chunk-2-2.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/BayesSpikeSolver-class.html
docs/reference/BayesSpikeSolver.html
docs/reference/CandidateFilter-class.html
docs/reference/EnsembleSolver-class.html
docs/reference/EnsembleSolver.html
docs/reference/FootprintFilter-class.html
docs/reference/FootprintFinder-class.html
docs/reference/GeneOntologyFilter-class.html
docs/reference/HumanDHSFilter-class.html
docs/reference/LassoPVSolver-class.html
docs/reference/LassoPVSolver.html
docs/reference/LassoSolver-class.html
docs/reference/LassoSolver.html
docs/reference/MotifMatcher-class.html
docs/reference/PCAMax.html
docs/reference/PearsonSolver-class.html
docs/reference/PearsonSolver.html
docs/reference/RandomForestSolver-class.html
docs/reference/RandomForestSolver.html
docs/reference/RidgeSolver-class.html
docs/reference/RidgeSolver.html
docs/reference/Solver-class.html
docs/reference/SpearmanSolver-class.html
docs/reference/SpearmanSolver.html
docs/reference/SqrtLassoSolver-class.html
docs/reference/SqrtLassoSolver.html
docs/reference/Trena-class.html
docs/reference/VarianceFilter-class.html
docs/reference/XGBoostSolver-class.html
docs/reference/XGBoostSolver.html
docs/reference/addStats.html
docs/reference/addStatsSimple.html
docs/reference/assessSnp.html
docs/reference/closeDatabaseConnections.html
docs/reference/createGeneModelFromRegulatoryRegions.html
docs/reference/createGeneModelFromTfList.html
docs/reference/elasticNetSolver.html
docs/reference/findMatchesByChromosomalRegion.html
docs/reference/getAssayData.html
docs/reference/getAvailableSolvers.html
docs/reference/getCandidates-FootprintFilter-method.html
docs/reference/getCandidates-GeneOntologyFilter-method.html
docs/reference/getCandidates-HumanDHSFilter-method.html
docs/reference/getCandidates-VarianceFilter-method.html
docs/reference/getCandidates.html
docs/reference/getChromLoc.html
docs/reference/getCoverage.html
docs/reference/getEncodeRegulatoryTableNames-HumanDHSFilter.html
docs/reference/getFootprintsForGene.html
docs/reference/getFootprintsInRegion.html
docs/reference/getGeneModelTableColumnNames.html
docs/reference/getGenePromoterRegion.html
docs/reference/getGtfGeneBioTypes.html
docs/reference/getGtfMoleculeTypes.html
docs/reference/getPfms.html
docs/reference/getPromoterRegionsAllGenes.html
docs/reference/getProximalPromoter.html
docs/reference/getRegulators.html
docs/reference/getRegulatoryChromosomalRegions.html
docs/reference/getRegulatoryRegions.html
docs/reference/getRegulatoryTableColumnNames.html
docs/reference/getSequence.html
docs/reference/getSolverNames.html
docs/reference/getTarget.html
docs/reference/index.html
docs/reference/normalizeModel.html
docs/reference/parseChromLocString.html
docs/reference/parseDatabaseUri.html
docs/reference/rescalePredictorWeights.html
docs/reference/run.html
docs/reference/show-HumanDHSFilter-method.html
docs/reference/show.BayesSpikeSolver.html
docs/reference/show.EnsembleSolver.html
docs/reference/show.LassoPVSolver.html
docs/reference/show.LassoSolver.html
docs/reference/show.MotifMatcher.html
docs/reference/show.PearsonSolver.html
docs/reference/show.RandomForestSolver.html
docs/reference/show.RidgeSolver.html
docs/reference/show.SpearmanSolver.html
docs/reference/show.SqrtLassoSolver.html
docs/reference/show.XGBoostSolver.html
docs/reference/solve.BayesSpike.html
docs/reference/solve.Ensemble.html
docs/reference/solve.Lasso.html
docs/reference/solve.LassoPV.html
docs/reference/solve.Pearson.html
docs/reference/solve.RandomForest.html
docs/reference/solve.Ridge.html
docs/reference/solve.Spearman.html
docs/reference/solve.SqrtLasso.html
docs/reference/solve.XGBoost.html
docs/reference/trena-package.html
inst/NEWS
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/tbl.mef2c.model.RData
inst/extdata/vrk2.neigborhood.hg38.footprints.db
inst/extdata/vrk2.neighborhood.hg38.gtfAnnotation.db
inst/extdata/xgboost.sample.RData
inst/extdata/yeast-53genes-536-samples.RData
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/unitTests/bugDemo001.R inst/unitTests/hidden_PCAMax.R
inst/unitTests/noTest_Trena.R-hidden
inst/unitTests/tbl.snps.RData
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_VarianceFilter.R inst/unitTests/test_XGBoostSolver.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/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/PCAMax.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-class.Rd man/VarianceFilter-class.Rd man/XGBoostSolver-class.Rd man/XGBoostSolver.Rd man/addStats.Rd man/addStatsSimple.Rd man/assessSnp.Rd man/closeDatabaseConnections.Rd man/createGeneModelFromRegulatoryRegions.Rd man/createGeneModelFromTfList.Rd man/elasticNetSolver.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/getCoverage.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/normalizeModel.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/show.XGBoostSolver.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 man/solve.XGBoost.Rd man/trena-package.Rd misc/nfe2/brand/brand-models.R
misc/nfe2/brand/trena.model.fimo.phast7.RData
misc/nfe2/brand/trena.models.brand.noDNA.RData
misc/nfe2/gtex-blood/gtex-blood-models.R
misc/nfe2/gtex-blood/trena.models.fimo.phast7.RData
misc/nfe2/gtex-blood/trena.models.noDNA
misc/nfe2/jaspar2018-hocomoco.meme
misc/nfe2/matchMotifs.R misc/nfe2/nfe2.R
misc/nfe2/tbls.motifs.RData
misc/paper.txt
tests/runTests.R vignettes/TReNA_Vignette.Rmd
vignettes/brand.tbl.model.trimmed
vignettes/caseStudyFour.Rmd vignettes/caseStudyOne.Rmd
vignettes/caseStudyOne.html
vignettes/caseStudyThree.Rmd vignettes/caseStudyTwo.Rmd
vignettes/caseStudyTwo.html
vignettes/igvR-nfe2-regulation-noGeneHancer.png
vignettes/igvR-nfe2-regulation.png
vignettes/makefile
vignettes/overview.Rmd vignettes/simple.Rmd vignettes/tiny.Rmd
PriceLab/TReNA documentation built on Nov. 20, 2019, 10:49 p.m.