__pycache__/
*.pyc
.venv/
*.egg-info/
.ruff_cache/
.mypy_cache/
.pytest_cache/
node_modules/
.next/
.env
*.db
.DS_Store

# Large data files
data/*.gz
data/*.gtf
data/*.fa
data/*.fai
data/*.csv
data/probes/
data/chromhmm/
data/gnomad/
data/hpa/
data/msigdb/
data/paxdb/
data/reactome/
data/repeatmasker/
data/herv/
data/clocks/
data/encode/
data/gwas/
.vercel

# Large reference/experiment data
data/tad/
data/hic/
data/wgbs/
data/accessibility/
data/pcawg/
data/replication/
data/insulation/
InSilicoExperiments/

# Unpublished manuscripts
docs/paper/
viewer/.superpowers/
