Welcome to phippery’s documentation!

Overview:

• Introduction
  • Getting Started
  • Background
  • References
  • Licensing and Acknowledgement
• Installation
  • Python API
  • Alignments Pipeline
  • Streamlit App
• Examples
  • Pan-CoV example dataset
  • Creating and running your own data

Nextflow Pipeline:

• Alignments Pipeline
• Input files
• Pipeline results
• Parameters
• Optional Parameters

Python API:

• Utils
• Normalize
• Modeling
• Eigen
• Escape Profile

Command Line Interface:

• Command Line Interface

Streamlit Viz App

• Streamlit Viz App

Methods Descriptions

• Comparing Escape Profiles
  • Introduction
  • Escape similarity score at a site
  • Escape similarity score for a region
  • References
• Background Modeling
  • Introduction
  • edgeR/BEER Method
  • Z-score Method (optional)
  • References

The Rest of It

• Gotchas
  • Missing Annotations (i.e. NaN’s)
• Contributing
  • Phippery Development Install
  • PyPI
  • Building Documentation
  • The Data Structure

Indices and tables

• Index

• Module Index

• Search Page