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

addStats | add PCA-based summary stats on all TFs in the model |

addStatsSimple | add PCA-based summary stats on all TFs in the model |

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 |

createGeneModelFromRegulatoryRegions | Create a model for a target gene using a Trena object |

createGeneModelFromTfList | Create a model for a target gene using a Trena object |

elasticNetSolver | Run the Elastic Net Solvers |

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 |

getCoverage | what percentage of the variance is captured in the first two... |

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 |

normalizeModel | transform a specific column to fit normal distribution |

parseChromLocString | Parse a string containing a chromosome and location on the... |

parseDatabaseUri | Parse a string containing the information for connecting to a... |

PCAMax | Class PCAMax |

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 |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.