# OS / Editor
.DS_Store
Thumbs.db
*.swp
.vscode/
.idea/

# Python
__pycache__/
*.pyc
*.pyo
.pytest_cache/
.ipynb_checkpoints/
*.egg-info/
.venv/
venv/
env/

# R
.Rhistory
.Rapp.history
.RData
.Ruserdata
*.Rproj.user/

# Data files (NEVER commit raw data — too large + may contain PII)
*.fastq
*.fastq.gz
*.fasta
*.bam
*.sam
*.h5ad
*.rds
*.tar
*.tar.gz
data/raw/

# Outputs (regenerable from scripts)
output/
*.csv
*.png
*.pdf
*.svg

# Keep these specific files even though pattern excludes
!requirements.txt
!data/SRA_BioSample_accession_mapping.csv
.requirements.txt.baiduyun.uploading.cfg
