🧬 nf-proteinactivity

Tool for generating gene expression signature and running viper for protein activity inference.

Contents

• 🧬 nf-proteinactivity
  • Contents
  • 🚀 Run Pipeline
    • 1. ⚡️ Full pipeline
    • 2. ✏️ Preprocessing Variants
      • Example
      • ⚡️ Optional Speed Improvements
    • 3. 🔮 Classifying Artifacts
    • 4. 🧠 Training/Retraining
  • Contributing

🚀 Run Pipeline

You need Nextflow installed.

nextflow run papaemmelab/nf-proteinactivity --help

Give it a try with a test run if you have docker available:

nextflow run papaemmelab/nf-proteinactivity -main -profile test,cloud

See this example:

nextflow run papaemmelab/nf-proteinactivity \
    -r main \
    --input {samplesheet.csv} \
    --outdir {results}

Contributing

Contributions are welcome, and they are greatly appreciated, check our contributing guidelines!