pyranges

Introduction

PyRanges is a Python library 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. It enables intuitive and highly efficient pipelines for genomic analysis.

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

Version 1.x

This is version 1.x of pyranges. It is a complete rewrite of the original pyranges library, that will replace the "default" (version 0) sometime in 2024.

Install

Pyranges 1.x requires python ≥3.12. Minimal installation:

pip install pyranges1

Installation including all optional dependencies:

pip install pyranges1[all]

Details at https://pyranges1.readthedocs.io/en/latest/installation.html

Documentation

The pyranges documentation, including installation instructions, API, tutorial, and how-to-pages, is available at https://pyranges1.readthedocs.io/

Features

• fast
• memory-efficient
• featureful
• pythonic/pandastic

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)

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://pyranges1.readthedocs.io/developer_guide.html