# piRNA Cluster Builder

## Documentation for package ‘PICB’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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