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| ExactSelect | Model for identifying erroneously linked pairs |
| gffToDataFrame | Generate a DataFrame of gene calls from a gff3 file |
| GlobalSelect | Model for identifying erroneously linked pairs |
| LinkedPairs-class | Tables of where syntenic hits link pairs of genes |
| LocalSelect | Model for identifying erroneously linked pairs |
| 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 |