Tools for Working With Synteny Objects


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Documentation for package ‘SynExtend’ version 1.6.0

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DisjointSet Return single linkage clusters from 'PairSummaries' objects.
EstimateRearrangementScenarios Estimate Genome Rearrangement Events with Double Cut and Join Operations
ExtractBy Extract and organize 'XStringSet's of sequences represented in a 'PairSummaries' object.
FindSets Find all single linkage clusters in an undirected pairs list.
Generic Model for predicting PID based on k-mer statistics
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
print.LinkedPairs Tables of where syntenic hits link pairs of genes
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