Tools for Working With Synteny Objects

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Documentation for package ‘SynExtend’ version 1.8.0

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

Help Pages

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 ProtWeaver Ensemble Models
DisjointSet	Return single linkage clusters from 'PairSummaries' objects.
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
EstimateRearrangementScenarios	Estimate Genome Rearrangement Events with Double Cut and Join Operations
EstimRearrScen	Estimate Genome Rearrangement Events with Double Cut and Join Operations
ExampleStreptomycesData	Example ProtWeaver Input Data from _Streptomyces_ Species
ExtractBy	Extract and organize 'DNAStringSets's.
FindSets	Find all single linkage clusters in an undirected pairs list.
Generic	Model for predicting PID based on k-mer statistics
GetProtWebData	Extract information from a ProtWeb object
GetProtWebData.ProtWeb	Extract information from a ProtWeb object
gffToDataFrame	Generate a DataFrame of gene calls from a gff3 file
LinkedPairs-class	Tables of where syntenic hits link pairs of genes
NucleotideOverlap	Tabulating Pairs of Genomic Sequences
PairSummaries	Summarize connected pairs in a LinkedPairs object
plot.ProtWeb	Plot predictions in a ProtWeb object
predict.ProtWeaver	Make predictions with ProtWeaver objects
print.LinkedPairs	Tables of where syntenic hits link pairs of genes
ProtWeaver	ProtWeaver: Predicting Protein Functional Association Networks
ProtWeaver-class	ProtWeaver: Predicting Protein Functional Association Networks
SequenceSimilarity	Return a numeric value that represents the similarity between two aligned sequences as determined by a provided subsitution matrix.
SubSetPairs	Subset a "PairSummaries" object.
[.LinkedPairs	Tables of where syntenic hits link pairs of genes