Fit transcriptional regulatory networks using gene expression, priors, machine learning

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 |

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 |

getAssayData | Retrieve the assay matrix of gene expression data from a... |

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 | Get Chromasome Location |

getFilterAssayData | Retrieve the assay matrix of gene expression data |

getFootprintsForGene | Get Footprints for Gene |

getFootprintsInRegion | Get Footprints in a Region |

getGenePromoterRegion | Get Gene Promoter Region |

getGtfGeneBioTypes | Get the List of Biotypes |

getGtfMoleculeTypes | Get the List of Molecule Types |

getPromoterRegionsAllGenes | Get Promoter Regions for All Genes |

getSolverName | Get the Solver Name from a TReNA Object |

getSolverObject | Get the Solver Object from a TReNA 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 |

mapMotifsToTFsMergeIntoTable | Map Motifs to Transcription Factors and Merge into a Table |

NullFilter-class | Create a NullFilter object |

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 |

solve | 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 |

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 | Class TReNA |

TReNA-package | Inferring Transcriptional Regulation with TReNA |

VarianceFilter-class | Create a VarianceFilter object |

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