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| DisjointSet | Return single linkage clusters from 'PairSummaries' objects. |
| 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 |
| [.LinkedPairs | Tables of where syntenic hits link pairs of genes |