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