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 |