# Tools for Working With Synteny Objects

## Documentation for package ‘SynExtend’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H J K L M N O P R S T W misc

## -- A --

AAHitScoping | Adjust the scope of kmer hits between feature and genome space.
Ancestral.EvoWeaver | Sequence Level Predictions for EvoWeaver
ApproximateBackground | Return the approximate background alignment score for a series of paired sequences.
as.data.frame.simMat | Similarity Matrices
as.dendrogram.DecisionTree | Decision Trees for Random Forests
as.matrix.simMat | Similarity Matrices
as.simMat | Similarity Matrices
as.simMat.matrix | Similarity Matrices
as.simMat.vector | Similarity Matrices

## -- B --

Behdenna.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
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 'PairSummaries' object.
BlockReconciliation | Rejection scheme for asyntenic predicted pairs
BuiltInEnsembles | Pretrained EvoWeaver Ensemble Models

## -- C --

CheckAgainstReport | Pull an assembly from the NCBI FTP site.
CIDist | Clustering Information Distance
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.
CorrGL.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver

## -- D --

DecisionTree-class | Decision Trees for Random Forests
dendrapply | Apply a Function to All Nodes of a Dendrogram
Diag | Similarity Matrices
Diag.simMat | Similarity Matrices
Diag<- | Similarity Matrices
Diag<-.simMat | Similarity Matrices
DisjointSet | Return single linkage clusters from 'PairSummaries' objects.
DPhyloStatistic | D-Statistic for Binary States on a Phylogeny

## -- E --

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
EstimateRearrangementScenarios | Estimate Genome Rearrangement Scenarios with Double Cut and Join Operations
EstimRearrScen | Estimate Genome Rearrangement Scenarios with Double Cut and Join Operations
EvoWeaver | EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
EvoWeaver-class | EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
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
EvoWeaver-utils | EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
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 'PairSummaries' object.
ExtantJaccard.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
ExtractBy | Extract and organize 'DNAStringSets's.

## -- F --

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

## -- G --

GeneDistance.EvoWeaver | Gene Organization Predictions for EvoWeaver
Generic | Model for predicting PID based on k-mer statistics
GeneVector.EvoWeaver | Sequence Level Predictions for EvoWeaver
gffToDataFrame | Generate a DataFrame of gene calls from a gff3 file
GLDistance.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
GLMI.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver

## -- H --

Hamming.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
HitConsensus | Return a numeric measure of whether kmer hits linking two genomic features are in linearly similar locations in both features.

## -- J --

JRFDist | Jaccard-Robinson-Foulds Distance and Nye Similarity

## -- K --

KFDist | Kuhner-Felsenstein Distance

## -- L --

LinkedPairs-class | Tables of where syntenic hits link pairs of genes

## -- M --

MakeBlastDb | Create a BLAST Database from R
MoranI | Moran's _I_ Spatial Autocorrelation Index
MoransI.EvoWeaver | Gene Organization Predictions for EvoWeaver

## -- N --

NormVec | Unit normalize a vector
NucleotideOverlap | Tabulating Pairs of Genomic Sequences

## -- O --

OneSite | Calculate a site on a right hyperbola.
OrientationMI.EvoWeaver | Gene Organization Predictions for EvoWeaver

## -- P --

PairSummaries | Summarize connected pairs in a LinkedPairs object
PAJaccard.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
PAOverlap.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver
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.DecisionTree | Decision Trees for Random Forests
plot.EvoWeb | Plot predictions in a EvoWeb object
predict.EvoWeaver | Make predictions with EvoWeaver objects
predict.RandForest | Classification and Regression with Random Forests
PrepareSeqs | Add feature sequences to Decipher databases.
print.LinkedPairs | Tables of where syntenic hits link pairs of genes
print.simMat | Similarity Matrices
ProfDCA.EvoWeaver | Phylogenetic Profiling Predictions for EvoWeaver

## -- R --

RandForest | Classification and Regression with Random Forests
RandForest.fit | Classification and Regression with Random Forests
RejectionBy | Given an object of candidate pairs, reject false positives.
RFDist | Robinson-Foulds Distance
RPContextTree.EvoWeaver | Phylogenetic Structure Predictions for EvoWeaver
RPMirrorTree.EvoWeaver | Phylogenetic Structure Predictions for EvoWeaver

## -- S --

SelectByK | Predicted pair trimming using K-means.
SequenceInfo.EvoWeaver | Sequence Level Predictions for EvoWeaver
SequenceSimilarity | Return a numeric value that represents the similarity between two aligned sequences as determined by a provided subsitution matrix.
simMat | Similarity Matrices
simMat-class | Similarity Matrices
SpeciesTree | EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
SpeciesTree.EvoWeaver | EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
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

## -- T --

TreeDistance.EvoWeaver | Phylogenetic Structure Predictions for EvoWeaver

## -- W --

WithinSetCompetition | Pare down candidate pairs to one-to-one sets.

## -- misc --

[.LinkedPairs | Tables of where syntenic hits link pairs of genes