| PICBannotate | Annotate GRanges according to a piRNA library |
| PICBbuild | Build piRNA seeds/cores/clusters from alignments |
| PICBexporttoexcel | Export cluster object into an Excel file |
| PICBgetchromosomes | Get SeqInfo object from standard non-circular chromosome names from your genome |
| PICBimportfromexcel | Import cluster object from an Excel file |
| PICBload | Load and preprocess BAM files containing piRNA alignments |
| PICBloadfasta | Get SeqInfo object from a fasta file |
| PICBoptimize | Runs PICBbuild multiple times with provided parameters and returns optimization data frame. |
| PICBstrandanalysis | Add sense/antisense ratio of unique piRNAs per piRNA cluster |