assessSnp | Assess the effect of a SNP using a Trena object |
BayesSpikeSolver | Create a Solver class object using the Bayes Spike Solver |
BayesSpikeSolver-class | An S4 class to represent a Bayes Spike solver |
CandidateFilter-class | CandidateFilter |
closeDatabaseConnections | Close a Footprint Database Connection |
createGeneModel | Create a model for a target gene using a Trena object |
EnsembleSolver | Create a Solver class object using an ensemble of solvers |
EnsembleSolver-class | Class EnsembleSolver |
findMatchesByChromosomalRegion | Find Motif Matches by Chromosomal Region |
FootprintFilter-class | Create a FootprintFilter object |
FootprintFinder-class | Class FootprintFinder |
GeneOntologyFilter-class | Create a GeneOntologyFilter object |
getAssayData | Retrieve the assay matrix of gene expression data from a... |
getAvailableSolvers | Get the available solvers for use in trena |
getCandidates | Get candidate genes using a CandidateFilter object |
getCandidates-FootprintFilter-method | Get candidate genes using the footprint filter |
getCandidates-GeneOntologyFilter-method | Get candidate genes using a gene ontology filter |
getCandidates-HumanDHSFilter-method | Get candidate genes using a human DHS filter |
getCandidates-VarianceFilter-method | Get candidate genes using the variance filter |
getChromLoc | Get Chromosome Location |
getEncodeRegulatoryTableNames-HumanDHSFilter | Get Encode regulatory tables using a human DHS filter |
getFootprintsForGene | Get Footprints for Gene |
getFootprintsInRegion | Get Footprints in a Region |
getGeneModelTableColumnNames | Retrieve the column names in the gene model table for a Trena... |
getGenePromoterRegion | Get Gene Promoter Region |
getGtfGeneBioTypes | Get the List of Biotypes |
getGtfMoleculeTypes | Get the List of Molecule Types |
getPfms | Retrieve the motifs from the pfms slot |
getPromoterRegionsAllGenes | Get Promoter Regions for All Genes |
getProximalPromoter | Grab the region of the proximal promoter for a given gene... |
getRegulators | Retrieve the candiate regulators from a Solver object |
getRegulatoryChromosomalRegions | Get the regulatory chromosomal regions for a Trena object |
getRegulatoryRegions | Get a tabel of regulatory regions for a Human DHS filter |
getRegulatoryTableColumnNames | Retrieve the column names in the regulatory table for a Trena... |
getSequence | Retrieve the Sequence for a Set of Regions |
getSolverNames | Retrieve the solver names from an EnsembleSolver object |
getTarget | Retrieve the target gene from a Solver object |
HumanDHSFilter-class | Create a HumanDHSFilter object |
LassoPVSolver | Create a Solver class object using the LASSO P-Value solver |
LassoPVSolver-class | An S4 class to represent a LASSO P-Value solver |
LassoSolver | Create a Solver class object using the LASSO solver |
LassoSolver-class | Class LassoSolver |
MotifMatcher-class | Create a MotifMatcher object |
parseChromLocString | Parse a string containing a chromosome and location on the... |
parseDatabaseUri | Parse a string containing the information for connecting to a... |
PearsonSolver | Create a Solver class object using Pearson correlation... |
PearsonSolver-class | An S4 class to represent a Pearson solver |
RandomForestSolver | Create a Solver class object using the Random Forest solver |
RandomForestSolver-class | Class RandomForestSolver |
rescalePredictorWeights | Rescale the Predictor Weights |
RidgeSolver | Create a Solver class object using the Ridge solver |
RidgeSolver-class | Class RidgeSolver |
run | Run a Solver object to select features |
show.BayesSpikeSolver | Show the Bayes Spike Solver |
show.EnsembleSolver | Show the Ensemble Solver |
show-HumanDHSFilter-method | Show the details of a human DHS filter |
show.LassoPVSolver | Show the Lasso PV Solver |
show.LassoSolver | Show the Lasso Solver |
show.MotifMatcher | Show a MotifMatcher object |
show.PearsonSolver | Show the Pearson Solver |
show.RandomForestSolver | Show the Random Forest Solver |
show.RidgeSolver | Show the Ridge Solver |
show.SpearmanSolver | Show the Spearman Solver |
show.SqrtLassoSolver | Show the Square Root Lasso Solver |
solve.BayesSpike | Run the Bayes Spike Solver |
solve.Ensemble | Run the Ensemble Solver |
solve.Lasso | Run the LASSO Solver |
solve.LassoPV | Run the LASSO P-Value Solver |
solve.Pearson | Run the Pearson Solver |
solve.RandomForest | Run the Random Forest Solver |
Solver-class | Define an object of class Solver |
solve.Ridge | Run the Ridge Regression Solver |
solve.Spearman | Run the Spearman Solver |
solve.SqrtLasso | Run the Square Root LASSO Solver |
SpearmanSolver | Create a Solver class object using Spearman correlation... |
SpearmanSolver-class | An S4 class to represent a Spearman solver |
SqrtLassoSolver | Create a Solver class object using the Square Root LASSO... |
SqrtLassoSolver-class | An S4 class to represent a Square Root LASSO solver |
Trena-class | Define an object of class Trena |
TReNA-package | Inferring Transcriptional Regulation with TReNA |
VarianceFilter-class | Create a VarianceFilter object |
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