Files in trena
Fit transcriptional regulatory networks using gene expression, priors, machine learning

_config.yml

NAMESPACE

DESCRIPTION

README.md tests/runTests.R

docs/pkgdown.css

docs/docsearch.css

docs/authors.html

docs/pkgdown.yml

docs/404.html

docs/docsearch.js

docs/pkgdown.js

docs/link.svg

docs/index.html

docs/articles/tiny.html

docs/articles/caseStudyThree.html

docs/articles/overview.html

docs/articles/TReNA_Vignette.html

docs/articles/caseStudyOne.html

docs/articles/simple.html

docs/articles/igvR-nfe2-regulation.png

docs/articles/index.html

docs/articles/nfe2-regulation-old.html

docs/articles/igvR-nfe2-regulation-noGeneHancer.png

docs/articles/caseStudyFour.html

docs/articles/caseStudyTwo.html

docs/articles/tiny_files/figure-html/unnamed-chunk-2-1.png

docs/articles/tiny_files/figure-html/unnamed-chunk-2-2.png

docs/articles/TReNA_Vignette_files/figure-html/unnamed-chunk-5-1.png

docs/articles/TReNA_Vignette_files/figure-html/unnamed-chunk-3-1.png

docs/articles/simple_files/figure-html/unnamed-chunk-2-1.png

docs/articles/simple_files/figure-html/unnamed-chunk-2-2.png

docs/reference/getChromLoc.html

docs/reference/EnsembleSolver.html

docs/reference/PearsonSolver.html

docs/reference/getGenePromoterRegion.html

docs/reference/RidgeSolver.html

docs/reference/solve.Pearson.html

docs/reference/RandomForestSolver-class.html

docs/reference/getRegulators.html

docs/reference/findMatchesByChromosomalRegion.html

docs/reference/Trena-class.html

docs/reference/getGeneModelTableColumnNames.html

docs/reference/SpearmanSolver-class.html

docs/reference/show.EnsembleSolver.html

docs/reference/show.SqrtLassoSolver.html

docs/reference/CandidateFilter-class.html

docs/reference/parseDatabaseUri.html

docs/reference/LassoPVSolver.html

docs/reference/FootprintFilter-class.html

docs/reference/getGtfGeneBioTypes.html

docs/reference/LassoSolver-class.html

docs/reference/solve.LassoPV.html

docs/reference/VarianceFilter-class.html

docs/reference/addStatsSimple.html

docs/reference/show.LassoSolver.html

docs/reference/getTarget.html

docs/reference/solve.Ensemble.html

docs/reference/SqrtLassoSolver.html

docs/reference/LassoSolver.html

docs/reference/PearsonSolver-class.html

docs/reference/trena-package.html

docs/reference/BayesSpikeSolver-class.html

docs/reference/show-HumanDHSFilter-method.html

docs/reference/getCoverage.html

docs/reference/getRegulatoryTableColumnNames.html

docs/reference/getProximalPromoter.html

docs/reference/addStats.html

docs/reference/LassoPVSolver-class.html

docs/reference/getFootprintsInRegion.html

docs/reference/RidgeSolver-class.html

docs/reference/getCandidates-FootprintFilter-method.html

docs/reference/getEncodeRegulatoryTableNames-HumanDHSFilter.html

docs/reference/createGeneModelFromTfList.html

docs/reference/XGBoostSolver-class.html

docs/reference/solve.Lasso.html

docs/reference/getGtfMoleculeTypes.html

docs/reference/show.RidgeSolver.html

docs/reference/getCandidates-GeneOntologyFilter-method.html

docs/reference/getAssayData.html

docs/reference/show.PearsonSolver.html

docs/reference/EnsembleSolver-class.html

docs/reference/getSolverNames.html

docs/reference/getCandidates.html

docs/reference/run.html

docs/reference/getRegulatoryChromosomalRegions.html

docs/reference/parseChromLocString.html

docs/reference/elasticNetSolver.html

docs/reference/Solver-class.html

docs/reference/getCandidates-HumanDHSFilter-method.html

docs/reference/RandomForestSolver.html

docs/reference/solve.XGBoost.html

docs/reference/FootprintFinder-class.html

docs/reference/XGBoostSolver.html

docs/reference/getSequence.html

docs/reference/MotifMatcher-class.html

docs/reference/getAvailableSolvers.html

docs/reference/HumanDHSFilter-class.html

docs/reference/normalizeModel.html

docs/reference/getPfms.html

docs/reference/solve.SqrtLasso.html

docs/reference/BayesSpikeSolver.html

docs/reference/assessSnp.html

docs/reference/SqrtLassoSolver-class.html

docs/reference/show.LassoPVSolver.html

docs/reference/show.XGBoostSolver.html

docs/reference/createGeneModelFromRegulatoryRegions.html

docs/reference/show.SpearmanSolver.html

docs/reference/index.html

docs/reference/GeneOntologyFilter-class.html

docs/reference/getRegulatoryRegions.html

docs/reference/show.MotifMatcher.html

docs/reference/SpearmanSolver.html

docs/reference/PCAMax.html

docs/reference/getCandidates-VarianceFilter-method.html

docs/reference/closeDatabaseConnections.html

docs/reference/solve.Ridge.html

docs/reference/getFootprintsForGene.html

docs/reference/show.RandomForestSolver.html

docs/reference/solve.BayesSpike.html

docs/reference/show.BayesSpikeSolver.html

docs/reference/getPromoterRegionsAllGenes.html

docs/reference/rescalePredictorWeights.html

docs/reference/solve.Spearman.html

docs/reference/solve.RandomForest.html

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

misc/paper.txt

misc/installDependencies.R misc/nfe2/nfe2.R misc/nfe2/matchMotifs.R

misc/nfe2/jaspar2018-hocomoco.meme

misc/nfe2/tbls.motifs.RData

misc/nfe2/gtex-blood/gtex-blood-models.R

misc/nfe2/gtex-blood/trena.models.noDNA

misc/nfe2/gtex-blood/trena.models.fimo.phast7.RData

misc/nfe2/brand/brand-models.R

misc/nfe2/brand/trena.models.brand.noDNA.RData

misc/nfe2/brand/trena.model.fimo.phast7.RData

inst/NEWS

inst/demos/test.png

inst/demos/Assess_Distributions.ipynb

inst/demos/findTFs.R inst/demos/demoEnhancersDatabaseOnWhovian.R inst/demos/findPiez02RegulatorySnps.R inst/demos/runLassoSolver.R inst/demos/trem2/go.R inst/utils/test_runTReNA.R inst/utils/extraFunctions.R

inst/utils/currentDBs.html

inst/utils/TReNA.R inst/utils/evaluateAllSolvers.R inst/utils/determineSqrtLambda.R inst/utils/runTReNA.R inst/utils/test_TReNA.R inst/utils/NaiveSolver.R inst/utils/createGlobusTable.R inst/utils/additionalTReNATests.R inst/utils/createGenomeScaleModel.R inst/utils/test_NaiveSolver.R inst/misc/assessSnp.R inst/misc/makeTRN-proximalanddistal-demo.R inst/misc/monteCarloTRN.R inst/misc/makeTRN-proximalonly-demo.R inst/misc/profileDbQueries.R inst/misc/runTReNA-demo.R inst/misc/createSQLiteDB.R

inst/misc/footprintFinding/piq/makefile

inst/misc/multiModels/style.js

inst/misc/multiModels/aqp4.R inst/misc/multiModels/aqp4-multi.R inst/misc/multiModels/graphToJSON-devel.R inst/unitTests/test_CandidateFilter.R inst/unitTests/test_VarianceFilter.R inst/unitTests/test_Solver.R inst/unitTests/test_HumanDHSFilter.R inst/unitTests/bugDemo001.R inst/unitTests/hidden_PCAMax.R

inst/unitTests/tbl.snps.RData

inst/unitTests/test_EnsembleSolver.R inst/unitTests/test_PearsonSolver.R inst/unitTests/test_RidgeSolver.R inst/unitTests/test_MotifMatcher.R inst/unitTests/test_LassoPVSolver.R inst/unitTests/test_SpearmanSolver.R inst/unitTests/test_FootprintFinder.R

inst/unitTests/noTest_Trena.R-hidden

inst/unitTests/test_FootprintFilter.R inst/unitTests/test_GeneOntologyFilter.R inst/unitTests/test_BayesSpikeSolver.R inst/unitTests/test_XGBoostSolver.R inst/unitTests/test_LassoSolver.R inst/unitTests/test_RandomForestSolver.R

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

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

inst/extdata/xgboost.sample.RData

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

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

inst/extdata/tbl.mef2c.model.RData

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

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/doc/tiny.Rmd

inst/doc/tiny.html

inst/doc/simple.Rmd inst/doc/caseStudyOne.Rmd

inst/doc/caseStudyThree.html

inst/doc/overview.Rmd inst/doc/caseStudyFour.Rmd inst/doc/TReNA_Vignette.R inst/doc/tiny.R inst/doc/TReNA_Vignette.Rmd

inst/doc/overview.html

inst/doc/caseStudyThree.Rmd inst/doc/caseStudyTwo.Rmd

inst/doc/TReNA_Vignette.html

inst/doc/caseStudyOne.html

inst/doc/overview.R inst/doc/simple.R

inst/doc/simple.html

inst/doc/caseStudyFour.html

inst/doc/caseStudyTwo.html

inst/notes/fillEnhancerDatabase.txt

build/vignette.rds

vignettes/makefile

vignettes/tiny.Rmd vignettes/simple.Rmd vignettes/caseStudyOne.Rmd vignettes/overview.Rmd vignettes/caseStudyFour.Rmd vignettes/TReNA_Vignette.Rmd vignettes/caseStudyThree.Rmd vignettes/caseStudyTwo.Rmd

vignettes/igvR-nfe2-regulation.png

vignettes/brand.tbl.model.trimmed

vignettes/igvR-nfe2-regulation-noGeneHancer.png

trena documentation built on Nov. 15, 2020, 2:07 a.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

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

Files in trena
Fit transcriptional regulatory networks using gene expression, priors, machine learning

R Package Documentation

Browse R Packages

We want your feedback!

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

Files in trena Fit transcriptional regulatory networks using gene expression, priors, machine learning

R Package Documentation

Browse R Packages

We want your feedback!

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

Files in trena
Fit transcriptional regulatory networks using gene expression, priors, machine learning