The pyranges0 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/pyranges0

Deprecation note

This repo currently hosts the “version 0” of pyranges. A redesigned, faster version 1 is available at https://github.com/pyranges/pyranges1 Version 1 will soon replace version 0. We encourage existing v0 users to migrate to v1 (see guide at https://pyranges1.readthedocs.io/en/latest/migration_guide.html), and new users to directly adopt v1. Read about v1 in our preprint at https://doi.org/10.64898/2025.12.11.693639

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.

Asking for help

If you encounter bugs, or the documentation is not enough and you cannot accomplish a specific task of interest, or if you’d like new features implemented, open an issue on GitHub: https://github.com/pyranges/pyranges0/issues