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Quick Start Guide

Get up and running with VCC-project in 5 minutes!

Prerequisites

# Check Python version (need 3.9+)
python --version

# Check mamba
mamba --version

Installation (2 minutes)

# 1. Clone repository
git clone https://github.com/ACTN3Bioinformatics/VCC-project.git
cd VCC-project

# 2. Create environment
mamba env create -f environment.yml

# 3. Activate environment
mamba activate vcc2025

Run Demo Pipeline (3 minutes)

# Download demo data
snakemake download_demo_data --cores 1

# Run complete pipeline
snakemake --cores 4 --configfile config/datasets.yaml

# View results
ls results/demo/

What Just Happened?

The pipeline:

  1. ✅ Downloaded ~10k cells from public Perturb-seq data
  2. ✅ Filtered low-quality cells (QC)
  3. ✅ Normalized and log-transformed counts
  4. ✅ Balanced perturbation classes
  5. ✅ Created train/val/test splits
  6. ✅ Generated QC reports

Explore Results

import scanpy as sc

# Load processed data
adata = sc.read_h5ad('results/demo/final.h5ad')

# Check it out
print(adata)
print(adata.obs['split'].value_counts())

Next Steps

  • 📖 Read PIPELINE_GUIDE.md for detailed documentation
  • 📓 Explore data interactively: jupyter notebook notebooks/demo_exploration.ipynb
  • 🔧 Customize parameters in config/datasets.yaml
  • 📊 Check QC report: reports/demo/qc_report.html
  • 🚀 Process your own data by adding to config/datasets.yaml

Interactive Data Exploration

Want to visualize and explore your data? Launch the demo notebook:

# Start Jupyter
jupyter notebook notebooks/demo_exploration.ipynb

# The notebook covers:
# - Loading processed data
# - QC metrics visualization
# - Perturbation analysis
# - PCA and UMAP plots
# - Gene expression patterns

Troubleshooting

Out of memory?

# In config/datasets.yaml, reduce:
demo:
  max_genes: 4000
  target_cells_per_perturbation: 50

Download failed?

# Manual download
wget https://zenodo.org/records/7041849/files/ReplogleWeissman2022_K562_essential.h5ad
mv ReplogleWeissman2022_K562_essential.h5ad data_local/demo/replogle_subset.h5ad

Need more help? See TROUBLESHOOTING.md