The pyranges documentation

Pyranges is a Python library specifically designed for efficient and intuitive manipulation of genomics data, particularly genomic intervals (like genes, genomic features, or reads). The library is optimized for fast querying and manipulation of genomic annotations.

Pyranges is open source, and hosted at github: https://github.com/pyranges/pyranges_1.x/

Pyranges is developed by Endre Bakken Stovner and by Marco Mariotti’s lab.

This documentation refers to the version 1 of pyranges, which introduces a new API and a new data structure compared to version 0, still the ‘default’, soon to be deprecated. If you are a pyranges v0 user, check this guide to migrate to v1.

Citation

Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918-919 http://dx.doi.org/10.1093/bioinformatics/btz615

Documentation outline

  1. 🚀 Installation instructions

  2. 🚀 The tutorial, recommended for all new users

  3. 🚀 The how-to pages, further below, where functionalities are grouped by topic

  4. 🚀 The API reference, where all methods are explained in detail

  5. 🚀 The developer guide, to follow in order to contribute to PyRanges

  6. 🚀 The guide to migrate to v1, for existing users of pyranges v0

Indices