How haaselab/picb works
PICB is an R toolkit for assembling and characterizing piRNA clusters. Its documented main workflow loads mapped piRNA alignments from a BAM against a reference genome, then builds seeds, cores, and clusters through stepwise integration. The package also exposes reference FASTA loading, annotation, optimization, strand analysis, chromosome lookup, and Excel import/export. Those capabilities are represented as separate entry points because their wiring is not established by the available README excerpt or source; edges show only the documented main workflow.
Main entry points: PICBbuild.R Cluster builder · PICBload.R Alignment loader · PICBloadfasta.R FASTA loader · PICBexporttoexcel.R Excel export
Components 17
Inputs
- Mapped BAM
- Reference genome
- FASTA loader
R/PICBloadfasta.R
Cluster assembly
- Alignment loader
R/PICBload.R - Loaded alignments
- Cluster builder
R/PICBbuild.R - Seeds
R/PICBbuild.R - Cores
R/PICBbuild.R - Clusters
R/PICBbuild.R
Cluster analysis
- Cluster annotation
R/PICBannotate.R - Cluster optimization
R/PICBoptimize.R - Strand analysis
R/PICBstrandanalysis.R - Chromosome lookup
R/PICBgetchromosomes.R
Data exchange
- Excel import
R/PICBimportfromexcel.R - Excel export
R/PICBexporttoexcel.R - Excel workbook
Other components
- PICB user
Connections 20
- PICB user → Alignment loader: loads data
- Mapped BAM → Alignment loader: reads alignments
- Reference genome → Alignment loader: uses reference
- PICB user → FASTA loader: loads reference
- FASTA loader → Reference genome: provides reference
- Alignment loader → Loaded alignments: returns alignments
- PICB user → Cluster builder: builds clusters
- Loaded alignments → Cluster builder: provides alignments
- Reference genome → Cluster builder: uses reference
- Cluster builder → Seeds: produces seeds
- Cluster builder → Cores: produces cores
- Cluster builder → Clusters: produces clusters
- PICB user → Cluster annotation: runs annotation
- PICB user → Cluster optimization: runs optimization
- PICB user → Strand analysis: analyzes strands
- PICB user → Chromosome lookup: looks up chromosomes
- PICB user → Excel import: imports data
- Excel workbook → Excel import: provides workbook
- PICB user → Excel export: exports data
- Excel export → Excel workbook: writes workbook