Welcome to SPRAS’s documentation!

SPRAS is a Python package that builds on Snakemake and Docker to provide a standardized, reproducible, and scalable framework for applying pathway reconstruction methods (PRMs) to omics data.

Getting Started

• About SPRAS
• Installing SPRAS
• Using SPRAS

Manual

• File formats
• Running with HTCondor

Supported Algorithms

• Pathway Reconstruction Methods

SPRAS API Docs For Developers

• spras

Contributing

• Contributing a new pathway reconstruction algorithm
• Maintaining SPRAS
• Patching Algorithms
• SPRAS Designs

Tutorials

• SPRAS Tutorial
• SPRAS Overview
• Beginner Tutorial - Set up & Running One Algorithm
• Intermediate Tutorial - Prepare Data & Multi-Algorithm Runs
• Advanced Capabilities and Features

Indices and tables

• Index

• Module Index

• Search Page