B C E F G L M N P R S T V misc
TReNA-package | Inferring Transcriptional Regulation with TReNA |
BayesSpikeSolver | Create a Solver class object using the Bayes Spike Solver |
BayesSpikeSolver-class | An S4 class to represent a Bayes Spike solver |
CandidateFilter | CandidateFilter |
CandidateFilter-class | CandidateFilter |
closeDatabaseConnections | Close a Footprint Database Connection |
closeDatabaseConnections-method | Close a Footprint Database Connection |
EnsembleSolver | Create a Solver class object using an ensemble of solvers |
EnsembleSolver-class | Class EnsembleSolver |
FootprintFilter | Create a FootprintFilter object |
FootprintFilter-class | Create a FootprintFilter object |
FootprintFinder | Class FootprintFinder |
FootprintFinder-class | Class FootprintFinder |
getAssayData | Retrieve the assay matrix of gene expression data from a Solver object |
getAssayData-method | Define an object of class Solver |
getCandidates | Get candidate genes using a CandidateFilter object |
getCandidates-FootprintFilter | Get candidate genes using the variance filter |
getCandidates-method | Get candidate genes using the variance filter |
getCandidates-method | Get candidate genes using the null filter |
getCandidates-method | Get candidate genes using the variance filter |
getCandidates-NullFilter | Get candidate genes using the null filter |
getCandidates-VarianceFilter | Get candidate genes using the variance filter |
getChromLoc | Get Chromasome Location |
getChromLoc-method | Get Chromasome Location |
getFilterAssayData | Retrieve the assay matrix of gene expression data |
getFilterAssayData-method | CandidateFilter |
getFootprintsForGene | Get Footprints for Gene |
getFootprintsForGene-method | Get Footprints for Gene |
getFootprintsInRegion | Get Footprints in a Region |
getFootprintsInRegion-method | Get Footprints in a Region |
getGenePromoterRegion | Get Gene Promoter Region |
getGenePromoterRegion-method | Get Gene Promoter Region |
getGtfGeneBioTypes | Get the List of Biotypes |
getGtfGeneBioTypes-method | Get the List of Biotypes |
getGtfMoleculeTypes | Get the List of Molecule Types |
getGtfMoleculeTypes-method | Get the List of Molecule Types |
getPromoterRegionsAllGenes | Get Promoter Regions for All Genes |
getPromoterRegionsAllGenes-method | Get Promoter Regions for All Genes |
getSolverName | Get the Solver Name from a TReNA Object |
getSolverName-method | Class TReNA |
getSolverObject | Get the Solver Object from a TReNA Object |
getSolverObject-method | Class TReNA |
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 |
mapMotifsToTFsMergeIntoTable | Map Motifs to Transcription Factors and Merge into a Table |
mapMotifsToTFsMergeIntoTable-method | Map Motifs to Transcription Factors and Merge into a Table |
NullFilter | Create a NullFilter object |
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 |
rescalePredictorWeights | Rescale the Predictor Weights |
rescalePredictorWeights-method | Rescale the Predictor Weights |
RidgeSolver | Create a Solver class object using the Ridge solver |
RidgeSolver-class | Class RidgeSolver |
run-method | Run the Bayes Spike Solver |
run-method | Run the Ensemble Solver |
run-method | Run the LASSO Solver |
run-method | Run the LASSO P-Value Solver |
run-method | Run the Pearson Solver |
run-method | Run the Random Forest Solver |
run-method | Run the Ridge Regression Solver |
run-method | Run the Spearman Solver |
run-method | Run the Square Root LASSO Solver |
run.BayesSpikeSolver | Run the Bayes Spike Solver |
run.EnsembleSolver | Run the Ensemble Solver |
run.LassoPVSolver | Run the LASSO P-Value Solver |
run.LassoSolver | Run the LASSO Solver |
run.PearsonSolver | Run the Pearson Solver |
run.RandomForestSolver | Run the Random Forest Solver |
run.RidgeSolver | Run the Ridge Regression Solver |
run.SpearmanSolver | Run the Spearman Solver |
run.SqrtLassoSolver | Run the Square Root LASSO Solver |
solve | Solve a TReNA Object |
solve-method | Solve a TReNA Object |
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 |
solve.Ridge | Run the Ridge Regression Solver |
solve.Spearman | Run the Spearman Solver |
solve.SqrtLasso | Run the Square Root LASSO Solver |
solve.TReNA | Solve a TReNA Object |
Solver | Define an object of class Solver |
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 TReNA |
TReNA-class | Class TReNA |
VarianceFilter | Create a VarianceFilter object |
VarianceFilter-class | Create a VarianceFilter object |
.BayesSpikeSolver | An S4 class to represent a Bayes Spike solver |
.CandidateFilter | CandidateFilter |
.EnsembleSolver | Class EnsembleSolver |
.FootprintFilter | Create a FootprintFilter object |
.FootprintFinder | Class FootprintFinder |
.LassoPVSolver | An S4 class to represent a LASSO P-Value solver |
.LassoSolver | Class LassoSolver |
.NullFilter | Create a NullFilter object |
.PearsonSolver | An S4 class to represent a Pearson solver |
.RandomForestSolver | Class RandomForestSolver |
.RidgeSolver | Class RidgeSolver |
.Solver | Define an object of class Solver |
.SpearmanSolver | An S4 class to represent a Spearman solver |
.SqrtLassoSolver | An S4 class to represent a Square Root LASSO solver |
.TReNA | Class TReNA |
.VarianceFilter | Create a VarianceFilter object |