HiChIP working methodology: alignment → valid pairs → QC → contact matrices → loop calling → visualization.
- docs/index.md — overview
- docs/prerequisites.md
- docs/input_files.md
- docs/prealignment.md
- docs/alignment_valid_pairs.md
- docs/qc.md
- docs/contact_matrix.md
- docs/loop_calling.md
- docs/visualization.md
- docs/references.md