Tools for Working With Synteny Objects


[Up] [Top]

Documentation for package ‘SynExtend’ version 1.8.0

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