GeneLab_benchmark/.gitignore at main · jang1563/GeneLab_benchmark · GitHub

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# ── Raw data downloads (3.4 GB) ──────────────────────────────────────────────
data/mouse/

# ── Processed expression matrices (828 MB) ───────────────────────────────────
# Normalized log2 counts — regenerate via normalize_*.R / fetch_osdr.py
processed/A_detection/
processed/B_cross_mission/
processed/C_cross_tissue/
processed/D_condition/
processed/J_pipeline/
processed/qc_reports/

# Keep pathway scores (small) and Ensembl map
!processed/pathway_scores/
!processed/fgsea/
!processed/ensembl_symbol_map.csv

# Full MSigDB fGSEA expansions are regenerable on HPC and kept out of Git
processed/fgsea/**/*_fgsea_c2cgp.csv
processed/fgsea/**/*_fgsea_c5bp.csv

# ── Task feature matrices (large train_X / test_X CSVs) ──────────────────────
# Labels, metadata, and fold structure are kept (small files)
tasks/**/train_X.csv
tasks/**/test_X.csv

# Intermediate/derived A1 task variants
tasks/A1_liver_lomo_combat/
tasks/A1_liver_lomo_iss_only/

# Geneformer token files (regenerate via geneformer_tokenize.py)
tasks/**/geneformer_tokens/

# ── Python artifacts ──────────────────────────────────────────────────────────
__pycache__/
*.py[cod]
*.pyo
.eggs/
*.egg-info/
dist/
build/

# Jupyter
.ipynb_checkpoints/
*.ipynb

# Virtual environments
.venv/
.hpc-venv/
venv/
env/
.conda/

# ── R artifacts ───────────────────────────────────────────────────────────────
.Rdata
.Rhistory
.RData
*.rds
Rplots.pdf

# ── macOS ─────────────────────────────────────────────────────────────────────
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
Icon?

# ── Editor / IDE ─────────────────────────────────────────────────────────────
.vscode/
.idea/
*.swp
*.swo
*~

# ── Logs and temporary files ──────────────────────────────────────────────────
*.log
*.tmp
*.temp
.genelab_staged*.txt
slurm-*.out
slurm-*.err

# ── v3 artifacts (large/binary) ──────────────────────────────────────────────
v3/evaluation/*.npy
v3/logs/
v3/processed/

# ── v8 external caches / generated artifacts ─────────────────────────────────
v8/bridge/geo_cache/
v8/**/__pycache__/

# ── Secrets / credentials ─────────────────────────────────────────────────────
.env
*.key
*.pem

# ── Internal planning / development docs (not for public repo) ────────────────
.claude/
PLAN.md
PLAN_*.md
**/PLAN_*.md
**/PLAN_V*.md
**/IMPROVEMENT_PLAN.md
**/PLAN_REVIEW*.md
**/RRRM1_DOWNSTREAM_PLAN*.md
**/RRRM1_SC_BENCHMARK_PLAN*.md
DESIGN_DECISIONS.md
docs/development_history/
v5/data/