Files in PriceLab/TReNA
Fit transcriptional regulatory networks using gene expression, priors, machine learning

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/BicorSolver.R R/CandidateFilter.R R/EnsembleSolver.R R/FeatureTable.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/Trena.R R/VarianceFilter.R R/XGBoostSolver.R R/help.R R/sharedFunctions.R R/utils.R README.md

_config.yml

docker/Dockerfile.1

docker/Dockerfile.2

docker/Dockerfile.3

docker/components/.bashrc

docker/components/installPackages-1.R docker/components/installPackages-2.R docker/components/ndufs2-demo.R

docker/components/ndufs2/data/gtex.brain.eqtls.chr1-160684126-161688825.RData

docker/components/ndufs2/data/haploreg-rs4575098-0.2.tsv

docker/components/ndufs2/data/mayoAllPeaks.merged.96064x4.RData

docker/components/ndufs2/data/rosmap.eqtls.RData

docker/components/ndufs2/data/tbl.fimo.NDUFS2.RData

docker/components/ndufs2/data/tbl.pairedEnd.small.NDUFS2.RData

docker/components/ndufs2/ndufs2.R docker/components/test_FeatureTable.R

docker/inputs/data/Brain_Cortex.RData

docker/inputs/data/gtex.brain.eqtls.chr1-160684126-161688825.RData

docker/inputs/data/haploreg-rs4575098-0.2.tsv

docker/inputs/data/mayoAllPeaks.merged.96064x4.RData

docker/inputs/data/rosmap.eqtls.RData

docker/inputs/data/tbl.fimo.NDUFS2.RData

docker/inputs/data/tbl.pairedEnd.small.NDUFS2.RData

docker/inputs/ndufs2.R

docker/makefile

docker/makefile-friday

docker/results/NDUFS2-results.tsv

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

explore/featureTables/zbtb7a/buildFeatureTable.R explore/featureTables/zbtb7a/fetch-eqtls.R explore/shiny/datatable/app.R

inst/NEWS

inst/demos/Assess_Distributions.ipynb

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

inst/demos/ndufs2/data/Brain_Cortex.RData

inst/demos/ndufs2/data/gtex.brain.eqtls.chr1-160684126-161688825.RData

inst/demos/ndufs2/data/haploreg-rs4575098-0.2.tsv

inst/demos/ndufs2/data/mayoAllPeaks.merged.96064x4.RData

inst/demos/ndufs2/data/rosmap.eqtls.RData

inst/demos/ndufs2/data/tbl.fimo.NDUFS2.RData

inst/demos/ndufs2/data/tbl.pairedEnd.small.NDUFS2.RData

inst/demos/ndufs2/ndufs2.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/brand.tbl.model.trimmed.RData

inst/extdata/featureTable/eqtls.ndufs2.hg19.RData

inst/extdata/featureTable/rna-seq.ndufs2.cor-gtex-cortex.RData

inst/extdata/featureTable/tbl.fimo-ndufs2-47kb.RData

inst/extdata/featureTable/tbl.haploreg.european.rs4575098.RData

inst/extdata/featureTableFimoTable.79611x9.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/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

makefile

man/BicorSolver-class.Rd man/BicorSolver.Rd man/CandidateFilter-class.Rd man/EnsembleSolver-class.Rd man/EnsembleSolver.Rd man/FeatureTable.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/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.BicorSolver.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.XGBoostSolver.Rd man/solve.Bicor.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.XGBoost.Rd man/trena-package.Rd misc/installDependencies.R 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

prep/featureTable/get-eQTLs.R prep/featureTable/get-rnaseq-correlation.R tests/runTests.R tools/buildFeatureTable.R vignettes/TReNA_Vignette.Rmd 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.R vignettes/overview.Rmd

vignettes/overview.html

vignettes/simple.Rmd vignettes/tiny.Rmd

PriceLab/TReNA documentation built on March 21, 2023, 1:57 p.m.

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PriceLab/TReNA
Fit transcriptional regulatory networks using gene expression, priors, machine learning

Files in PriceLab/TReNA
Fit transcriptional regulatory networks using gene expression, priors, machine learning

R Package Documentation

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We want your feedback!

PriceLab/TReNA Fit transcriptional regulatory networks using gene expression, priors, machine learning

Files in PriceLab/TReNA Fit transcriptional regulatory networks using gene expression, priors, machine learning

R Package Documentation

Browse R Packages

We want your feedback!

PriceLab/TReNA
Fit transcriptional regulatory networks using gene expression, priors, machine learning

Files in PriceLab/TReNA
Fit transcriptional regulatory networks using gene expression, priors, machine learning