API for npcooley/SynExtend
Tools for Working With Synteny Objects
| Global functions | |
|---|---|
| .safecheck_numeric | Source code |
| AdjMatToDf | Source code |
| Ancestral | Source code |
| Ancestral.EvoWeaver | Man page Source code |
| Behdenna | Source code |
| Behdenna.EvoWeaver | Man page Source code |
| BlastSeqs | Man page Source code |
| BlockExpansion | Man page Source code |
| BlockReconciliation | Man page Source code |
| BuildSimMatInternal | Source code |
| BuiltInEnsembles | Man page |
| CIDist | Man page Source code |
| CIDist_NullDist | Man page |
| CalcMIReduced | Source code |
| CheckBifurcating | Source code |
| ClusterByK | Man page Source code |
| ConcatSeqs | Source code |
| CophProfiles | Source code |
| CophProfiles.EvoWeaver | Source code |
| CorrComp_C | Source code |
| CorrCompressSeqs | Source code |
| CorrGL | Source code |
| CorrGL.EvoWeaver | Man page Source code |
| DCA_gradient_minimize_fxn | Source code |
| DCA_logRISE | Source code |
| DCA_logrise_run | Source code |
| DCA_minimize_fxn | Source code |
| DPhyloStatistic | Man page Source code |
| DecisionTree-class | Man page |
| Diag | Man page Source code |
| Diag.simMat | Man page Source code |
| Diag<- | Man page |
| Diag<-.simMat | Man page |
| DisjointSet | Man page Source code |
| Endosymbionts_GeneCalls | Man page |
| Endosymbionts_LinkedFeatures | Man page |
| Endosymbionts_Pairs01 | Man page |
| Endosymbionts_Pairs02 | Man page |
| Endosymbionts_Pairs03 | Man page |
| Endosymbionts_Sets | Man page |
| Endosymbionts_Synteny | Man page |
| Ensemble | Source code |
| EstimRearrScen | Man page Source code |
| EstimateExoLabel | Man page Source code |
| EstimateRearrangementScenarios | Man page |
| EvoWeaver | Man page Source code |
| EvoWeaver-GOPreds | Man page |
| EvoWeaver-PPPreds | Man page |
| EvoWeaver-PSPreds | Man page |
| EvoWeaver-SLPreds | Man page |
| EvoWeaver-class | Man page |
| EvoWeaver-utils | Man page |
| EvoWeaverEnsemblePrediction | Source code |
| EvoWeb | Man page |
| EvoWebMatToDf | Source code |
| ExampleStreptomycesData | Man page |
| ExoLabel | Man page Source code |
| ExpandDiagonal | Man page Source code |
| ExtantJaccard | Source code |
| ExtantJaccard.EvoWeaver | Man page Source code |
| ExtractBy | Man page Source code |
| FastDend | Source code |
| FastQFromSRR | Man page Source code |
| FindSets | Man page Source code |
| FitchParsimony | Man page Source code |
| GLDistance | Source code |
| GLDistance.EvoWeaver | Man page Source code |
| GLMI | Source code |
| GLMI.EvoWeaver | Man page Source code |
| GeneDistance | Source code |
| GeneDistance.EvoWeaver | Man page Source code |
| GeneVector | Source code |
| GeneVector.EvoWeaver | Man page Source code |
| Generic | Man page |
| Hamming | Source code |
| Hamming.EvoWeaver | Man page Source code |
| HungarianAssignment | Source code |
| JRFDist | Man page Source code |
| KFDist | Man page Source code |
| LanczosEigen | Source code |
| LinkedPairs-class | Man page |
| MICalc_C | Source code |
| MISeqLevel | Source code |
| MakeBlastDb | Man page Source code |
| MoranI | Man page Source code |
| MoransI | Source code |
| MoransI.EvoWeaver | Man page Source code |
| MutualInformationPA.EvoWeaver | Source code |
| NormArgProcessors | Source code |
| NucleotideOverlap | Man page Source code |
| OldEnsemble.EvoWeaver | Source code |
| OrientationMI | Source code |
| OrientationMI.EvoWeaver | Man page Source code |
| PAJaccard | Source code |
| PAJaccard.EvoWeaver | Man page Source code |
| PAOverlap | Source code |
| PAOverlap.EvoWeaver | Man page Source code |
| PAPV | Source code |
| PAPV.EvoWeaver | Source code |
| PAProfiles | Source code |
| PAProfiles.EvoWeaver | Source code |
| PAStats | Source code |
| PairSummaries | Man page Source code |
| PhyloDistance | Man page Source code |
| PhyloDistance-CI | Man page |
| PhyloDistance-JRF | Man page |
| PhyloDistance-KF | Man page |
| PhyloDistance-RF | Man page |
| PrepareSeqs | Man page Source code |
| ProcessSubset | Source code |
| ProfDCA.EvoWeaver | Man page |
| ProfileDCA | Source code |
| ProfileDCA.EvoWeaver | Source code |
| RFDist | Man page Source code |
| RPContextTree | Source code |
| RPContextTree.EvoWeaver | Man page Source code |
| RPMirrorTree | Source code |
| RPMirrorTree.EvoWeaver | Man page Source code |
| RandCophProfiles | Source code |
| RandCophProfiles.EvoWeaver | Source code |
| RandForest | Man page Source code |
| RandForest.fit | Man page Source code |
| ResidueMIDend | Source code |
| ResidueMISeqs | Source code |
| SelectByK | Man page Source code |
| SequenceInfo | Source code |
| SequenceInfo.EvoWeaver | Man page Source code |
| SequenceSimilarity | Man page Source code |
| ShuffleC | Source code |
| ShuffleWithRecomb | Source code |
| SpeciesTree | Man page Source code |
| SpeciesTree.EvoWeaver | Man page Source code |
| Standardize_Subset | Source code |
| SubSetPairs | Man page Source code |
| SummarizePairs | Man page Source code |
| SuperTree | Man page Source code |
| SuperTreeEx | Man page |
| TreeDistance | Source code |
| TreeDistance.EvoWeaver | Man page Source code |
| [.LinkedPairs | Man page |
| `Diag<-.simMat` | Source code |
| `Diag<-` | Source code |
| `[.EvoWeaver` | Source code |
| `[.LinkedPairs` | Source code |
| `[.simMat` | Source code |
| `[<-.simMat` | Source code |
| `names<-.simMat` | Source code |
| as.data.frame.EvoWeb | Source code |
| as.data.frame.simMat | Man page Source code |
| as.dendrogram.DecisionTree | Man page Source code |
| as.matrix.EvoWeb | Source code |
| as.matrix.simMat | Man page Source code |
| as.simMat | Man page Source code |
| as.simMat.default | Source code |
| as.simMat.matrix | Man page Source code |
| as.simMat.vector | Man page Source code |
| calc_SId_mat | Source code |
| combineDist | Source code |
| dendrapply | Man page Source code |
| dineof | Source code |
| fastCoph | Source code |
| findSpeciesTree | Source code |
| find_dend_distances | Source code |
| find_dists_pos | Source code |
| fitch_down | Source code |
| fitch_parsimony | Source code |
| fitch_up | Source code |
| flatdendrapply | Source code |
| gain_loss_vec | Source code |
| generateGainLossVec | Source code |
| gffToDataFrame | Man page Source code |
| initDTStructure | Source code |
| names.simMat | Source code |
| new_EvoWeaver | Source code |
| pair_residues | Source code |
| plot.DecisionTree | Man page Source code |
| plot.EvoWeb | Man page Source code |
| predict.EvoWeaver | Man page Source code |
| predict.RandForest | Man page Source code |
| predictWithBuiltins | Source code |
| print.DecisionTree | Source code |
| print.EvoWeaver | Source code |
| print.EvoWeb | Source code |
| print.GenRearr | Source code |
| print.LinkedPairs | Man page Source code |
| print.RandForest | Source code |
| print.simMat | Man page Source code |
| recursive_parentdendrapply | Source code |
| rowSumsOfDist | Source code |
| show.DecisionTree | Source code |
| show.EvoWeaver | Source code |
| show.EvoWeb | Source code |
| show.RandForest | Source code |
| show.simMat | Source code |
| simMat | Man page Source code |
| simMat-class | Man page |
| subset.dendrogram | Man page Source code |
| summary.EvoWeb | Source code |
| trim_paralogs | Source code |
| validate_EvoWeaver | Source code |
| validate_EvoWeaver_methods | Source code |
