pyranges

Introduction

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.

"Finally ... This was what Python badly needed for years." - Heng Li

Deprecation note!

This repo currently hosts the "version 0" of pyranges. A redesigned, faster version1 is available at https://github.com/pyranges/pyranges_1.x 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

Documentation

The pyranges documentation, including installation instructions, API, tutorial, and how-to-pages, of version 0 is available at https://pyranges.readthedocs.io/

Features

• fast
• memory-efficient
• featureful
• pythonic/pandastic
• supports chaining with a terse syntax
• uses Pandas DataFrames, so the whole Python data science stack works on PyRanges

Paper/Cite

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

Supporting pyranges

• most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
• use pyranges in Stack Overflow/biostars questions and answers
• star the repo (possibly important for github visibility and as a proxy for project popularity)
• if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/

Asking for help

If you encounter bugs, or the documentation is not enough a cannot accomplish a specific task of interest, or if you'd like new features implemented, open an Issue at github: https://github.com/pyranges/pyranges/issues

Contributing to pyranges

Pyranges accepts code contributions in form of pull request. For details, visit https://pyranges.readthedocs.io/developer_guide.html