Tools for Working With Synteny Objects

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Documentation for package ‘SynExtend’ version 1.16.0

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

Help Pages

Ancestral.EvoWeaver	Sequence-Level Predictions for EvoWeaver
as.data.frame.simMat	Similarity Matrices
as.matrix.simMat	Similarity Matrices
as.simMat	Similarity Matrices
as.simMat.matrix	Similarity Matrices
as.simMat.vector	Similarity Matrices
Behdenna.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
BlastSeqs	Run BLAST queries from R
BlockExpansion	Attempt to expand blocks of paired features in a 'PairSummaries' object.
BlockReconciliation	Rejection scheme for asyntenic predicted pairs
BuiltInEnsembles	Pretrained EvoWeaver Ensemble Models
CIDist	Clustering Information Distance
CIDist_NullDist	Simulated Null Distributions for CI Distance
ClusterByK	Predicted pair trimming using K-means.
Coloc.EvoWeaver	Gene Organization Predictions for EvoWeaver
ColocMoran.EvoWeaver	Gene Organization Predictions for EvoWeaver
ContextTree.EvoWeaver	Phylogenetic Structure Predictions for EvoWeaver
CorrGL.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
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
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 Events with Double Cut and Join Operations
EstimRearrScen	Estimate Genome Rearrangement Events with Double Cut and Join Operations
EvoWeaver	EvoWeaver: Predicting Protein Functional Association Networks
EvoWeaver-class	EvoWeaver: Predicting Protein Functional Association Networks
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: Predicting Protein Functional Association Networks
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.
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
GainLoss.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
Generic	Model for predicting PID based on k-mer statistics
gffToDataFrame	Generate a DataFrame of gene calls from a gff3 file
Hamming.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
Jaccard.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
JRFDist	Jaccard-Robinson-Foulds Distance
KFDist	Kuhner-Felsenstein Distance
LinkedPairs-class	Tables of where syntenic hits link pairs of genes
MakeBlastDb	Create a BLAST Database from R
MirrorTree.EvoWeaver	Phylogenetic Structure Predictions for EvoWeaver
MoransI	Moran's _I_ Spatial Autocorrelation Index
MutualInformation.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
NucleotideOverlap	Tabulating Pairs of Genomic Sequences
NVDT.EvoWeaver	Sequence-Level Predictions for EvoWeaver
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
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	Return gene sequences.
print.LinkedPairs	Tables of where syntenic hits link pairs of genes
print.simMat	Similarity Matrices
ProfDCA.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
ResidueMI.EvoWeaver	Sequence-Level Predictions for EvoWeaver
RFDist	Robinson-Foulds Distance
SelectByK	Predicted pair trimming using K-means.
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: Predicting Protein Functional Association Networks
SpeciesTree.EvoWeaver	EvoWeaver: Predicting Protein Functional Association Networks
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
TranscripMI.EvoWeaver	Gene Organization Predictions for EvoWeaver
TreeDistance.EvoWeaver	Phylogenetic Structure Predictions for EvoWeaver
[.LinkedPairs	Tables of where syntenic hits link pairs of genes