Pharmacogenomics Prediction Pipeline (P3)

Overview

The P3 pipeline aims to predict drug sensitivity utilizing second-generation sequencing data and biological annotation (gene ontology, pathways, etc.), and in vitro high-throughput drug screening data.

Contents:

• Installation
• Configuration
  • Config sections
  • Example config.yaml
• P3 features
  • norm_counts.snakefile
  • zscores.snakefile
  • variants.snakefile
  • cnv.snakefile
  • Pathways
• Filtering features and responses
  • Filtering samples and responses
• Pipeline design
  • Overview
  • Adding a new feature set
  • Creating the snakefiles
• Obtaining pathway scores
• Documentation about the documentation
  • Run the pipeline on example data
  • Run build-docs.sh
  • Merge master with gh-pages branch
  • Make the docs while in the gh-pages branch
  • Check output and push to github
  • Switch back to master branch
  • View docs on web

Indices and tables

• Index
• Module Index
• Search Page