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| gtfToExons | Convert GTF file to exon location file |
| makeBranchpointWindowForExons | Make branchpoint window regions |
| makeBranchpointWindowForSNP | Makes a branchpointer formatted GRanges object from refsnp ids |
| plotBranchpointWindow | Plots branchpointer predictions |
| predictBranchpoints | Predict branchpoint probability scores |
| predictionsToSummary | Convert SNP branchpoint predictions across the branchpoint window to an intronic summary |
| readQueryFile | Read a query file |