Metadata-Version: 2.1
Name: pyranges
Version: 0.1.0
Summary: GenomicRanges for Python.
Author-email: Endre Bakken Stovner <endbak@pm.me>
License: MIT
Project-URL: Homepage, http://github.com/pyranges/pyranges
Keywords: bioinformatics,genomicranges,genomics
Classifier: Programming Language :: Python :: 3
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Other Environment
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Topic :: Scientific/Engineering
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Description-Content-Type: text/markdown
License-File: LICENSE
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Provides-Extra: add-ons
Requires-Dist: pyrle>=0.0.39; extra == "add-ons"
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Requires-Dist: pyranges[dev]; extra == "all"
Requires-Dist: pyranges[docs]; extra == "all"

# pyranges

[![Coverage Status](https://img.shields.io/coveralls/github/biocore-ntnu/pyranges.svg)](https://coveralls.io/github/biocore-ntnu/pyranges?branch=master) [![hypothesis tested](graphs/hypothesis-tested-brightgreen.svg)](http://hypothesis.readthedocs.io/) [![PyPI version](https://badge.fury.io/py/pyranges.svg)](https://badge.fury.io/py/pyranges) [![MIT](https://img.shields.io/pypi/l/pyranges.svg?color=green)](https://opensource.org/licenses/MIT) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyranges.svg) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pyranges/README.html)

## Missing:

- to_bigwig: needs a rewrite of the pyrle module

## 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

## Documentation

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

## Features

  - fast
  - memory-efficient
  - featureful
  - pythonic/pandastic
  - supports chaining with a terse syntax
  - is a proper subclass of Pandas DataFrames

## 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://pyranges.readthedocs.io/developer_guide.html

