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
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
NullFilter-class        Create a NullFilter 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             Class TReNA
TReNA-package           Inferring Transcriptional Regulation with TReNA
VarianceFilter-class    Create a VarianceFilter object
closeDatabaseConnections,FootprintFinder-method
                        Close a Footprint Database Connection
getAssayData            Retrieve the assay matrix of gene expression
                        data from a Solver object
getCandidates           Get candidate genes using a CandidateFilter
                        object
getCandidates,FootprintFilter-method
                        Get candidate genes using the variance filter
getCandidates,NullFilter-method
                        Get candidate genes using the null filter
getCandidates,VarianceFilter-method
                        Get candidate genes using the variance filter
getChromLoc,FootprintFinder-method
                        Get Chromasome Location
getFilterAssayData      Retrieve the assay matrix of gene expression
                        data
getFootprintsForGene,FootprintFinder-method
                        Get Footprints for Gene
getFootprintsInRegion,FootprintFinder-method
                        Get Footprints in a Region
getGenePromoterRegion,FootprintFinder-method
                        Get Gene Promoter Region
getGtfGeneBioTypes,FootprintFinder-method
                        Get the List of Biotypes
getGtfMoleculeTypes,FootprintFinder-method
                        Get the List of Molecule Types
getPromoterRegionsAllGenes,FootprintFinder-method
                        Get Promoter Regions for All Genes
getSolverName           Get the Solver Name from a TReNA Object
getSolverObject         Get the Solver Object from a TReNA Object
mapMotifsToTFsMergeIntoTable,FootprintFinder-method
                        Map Motifs to Transcription Factors and Merge
                        into a Table
rescalePredictorWeights,Solver-method
                        Rescale the Predictor Weights
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
solve,TReNA-method      Solve a TReNA Object
