Tutorial

This tutorial provides an introduction to pyrpipe. New users can start here to get an idea of how to use pyrpipe APIs for RNA-Seq or other analysis. This tutorial is divided into smaller sections.

Section 1 describes the recommended way of installing pyrpipe and setting up conda environments.

Section 2 is an introduction to basic RNA-Seq API is provided via a simple RNA-Seq processing pipeline example.

Section 3 provides information on how to extend pipelines using third-party tools and integrate pyrpipe into snakemake for more scalable workflows.

Subsequent Sections detail pyrpipe_engine, pyrpipe_utils and pyrpipe_diagnostic, each of which provide helpful functionality.

• Setting up the environment
• Basic RNA-Seq processing
• Importing tools into python
• Building APIs
• Snakemake example
• RNA-Seq API
• pyrpipe_engine module
• pyrpipe_utils module
• pyrpipe_diagnostic