Welcome to pairk’s documentation!

repository link - https://github.com/jacksonh1/pairk

Getting Started

quick pairk startup guide

To the Getting Started Guide

PairK Tutorial

An in-depth guide for users.

To the PairK Tutorial

Examples

Examples using pairk and how to interpret the results

To the Examples

API Reference

PairK API. The docstrings of the main functions

To the API Reference.

References

references and acknowledgements

To the References

• Getting Started
  • Pairk Overview
  • quickstart
  • PairK’s main functions and classes
• Pairk - tutorial
  • introduction
  • import
  • load example data
  • Step 1: pairwise k-mer alignment
  • Step 2: k-mer conservation
  • advanced customization
• PairK examples - interpreting pairk conservation results
  • background scores and z-scores
  • background score standard deviation
• PairK alignment - in depth
  • Scoring matrix alignment
  • Embedding distance alignment
  • k-mer alignment results
• API Documentation
  • PairK convencience functions
  • pairwise k-mer alignment
  • k-mer conservation
  • utility functions
  • single k-mer functions
• References and acknowledgements
  • Additional references: