User Guide
Task-oriented walkthroughs for each subsystem. Each page assumes the concepts in Concepts and focuses on a single module.
| Module | What it’s for |
|---|---|
| Loci | Intervals, set algebra, merge/sort/slop/nearest. |
| Genes | Parse GTF / UCSC RefSeq; enhancer-to-gene assignment. |
| Architecture | Chromatin-contact graphs from loops + Hi-C. |
| Signal | Threaded bigWig extraction, TMM, heatmaps. |
| Browser | IGV-like SVG region plots. |
| BEDPE | Paired-end intervals / loop files. |
| Motifs | JASPAR motif scanning over FASTA genomes. |
| Atlas | GIGGLE-style enrichment against large BED collections (ChIP-Atlas). |