Man pages for npcooley/SynExtend
Tools for Comparative Genomics
| AAHitScoping | Adjust the scope of kmer hits between feature and genome... |
| ApproximateBackground | Return the approximate background alignment score for a... |
| BlastSeqs | Run BLAST queries from R |
| BlockByRank | Return simple summaries of blocks of candidate pairs. |
| BlockExpansion | Attempt to expand blocks of paired features in a... |
| BlockReconciliation | Rejection scheme for asyntenic predicted pairs |
| BuiltInEnsembles | Pretrained EvoWeaver Ensemble Models |
| CheckAgainstReport | Pull an assembly from the NCBI FTP site. |
| CIDist_NullDist | Simulated Null Distributions for CI Distance |
| ClusterByK | Predicted pair trimming using K-means. |
| CompetePairs | Find the best match pair in cases where ambiguity exists. |
| DecisionTree-class | Decision Trees for Random Forests |
| dendrapply | Apply a Function to All Nodes of a Dendrogram |
| DisjointSet | Return single linkage clusters from 'PairSummaries' objects. |
| DPhyloStatistic | D-Statistic for Binary States on a Phylogeny |
| Endosymbionts_GeneCalls | Example genecalls |
| Endosymbionts_LinkedFeatures | Example synteny links |
| Endosymbionts_Pairs01 | Example predicted pairs |
| Endosymbionts_Pairs02 | Example predicted pairs |
| Endosymbionts_Pairs03 | Example predicted pairs |
| Endosymbionts_Sets | A list of disjoint sets. |
| Endosymbionts_Synteny | A synteny object |
| EstimateExoLabel | Estimate ExoLabel Disk Consumption |
| EstimRearrScen | Estimate Genome Rearrangement Scenarios with Double Cut and... |
| EvoWeaver | EvoWeaver: Identifying Gene Functional Associations from... |
| EvoWeaver-GOPreds | Gene Organization Predictions for EvoWeaver |
| EvoWeaver-PPPreds | Phylogenetic Profiling Predictions for EvoWeaver |
| EvoWeaver-PSPreds | Phylogenetic Structure Predictions for EvoWeaver |
| EvoWeaver-SLPreds | Sequence Level Predictions for EvoWeaver |
| EvoWeb | EvoWeb: Predictions from EvoWeaver |
| ExampleStreptomycesData | Example EvoWeaver Input Data from _Streptomyces_ Species |
| ExoLabel | ExoLabel: Out-of-Memory Fast Label Propagation |
| ExpandDiagonal | Attempt to expand blocks of paired features in a... |
| ExtractBy | Extract and organize 'DNAStringSets's. |
| FastQFromSRR | Get Sequencing Data from the SRA |
| FindSets | Find all single linkage clusters in an undirected pairs list. |
| FitchParsimony | Calculate ancestral states using Fitch Parsimony |
| Generic | Model for predicting PID based on k-mer statistics |
| gffToDataFrame | Generate a DataFrame of gene calls from a gff3 file |
| HitConsensus | Return a numeric measure of whether kmer hits linking two... |
| LinkedPairs-class | Tables of where syntenic hits link pairs of genes |
| MakeBlastDb | Create a BLAST Database from R |
| MoransI | Moran's _I_ Spatial Autocorrelation Index |
| NormVec | Unit normalize a vector |
| NucleotideOverlap | Tabulating Pairs of Genomic Sequences |
| OneSite | Calculate a site on a right hyperbola. |
| PairSummaries | Summarize connected pairs in a LinkedPairs object |
| PhyloDistance | Calculate Distance between Unrooted Phylogenies |
| PhyloDistance-CI | Clustering Information Distance |
| PhyloDistance-JRF | Jaccard-Robinson-Foulds Distance and Nye Similarity |
| PhyloDistance-KF | Kuhner-Felsenstein Distance |
| PhyloDistance-RF | Robinson-Foulds Distance |
| plot.EvoWeb | Plot predictions in a EvoWeb object |
| predict.EvoWeaver | Make predictions with EvoWeaver objects |
| PrepareSeqs | Add feature sequences to Decipher databases. |
| RandForest | Classification and Regression with Random Forests |
| RejectionBy | Given an object of candidate pairs, reject false positives. |
| SelectByK | Predicted pair trimming using K-means. |
| SequenceSimilarity | Return a numeric value that represents the similarity between... |
| simMat | Similarity Matrices |
| subset-dendrogram | Subsetting dendrogram objects |
| SubSetPairs | Subset a "PairSummaries" object. |
| SummarizePairs | Provide summaries of hypothetical orthologs. |
| SuperTree | Create a Species Tree from Gene Trees |
| SuperTreeEx | Example Dendrograms |
| WithinSetCompetition | Pare down candidate pairs to one-to-one sets. |
