Metadata-Version: 2.4
Name: polyase
Version: 1.3.0
Summary: A package for analyzing allele-specific expression in polyploid organisms
License: MIT
License-File: LICENSE
Keywords: bioinformatics,polyploid,allele-specific,expression
Author: nadja.franziska.nolte@nib.si
Requires-Python: >=3.11,<3.13
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Provides-Extra: dev
Provides-Extra: docs
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Project-URL: Homepage, https://polyase.readthedocs.io/en/latest/
Project-URL: Issues, https://github.com/nadjano/polyase/issues
Project-URL: Repository, https://github.com/nadjano/polyase
Description-Content-Type: text/markdown

<img style="width: 50%;" alt="polyASE_logo" src="https://github.com/user-attachments/assets/4d3dea85-c1a6-4707-a498-0e969a5e6c07" />

# PolyASE

A Python package for analyzing allele-specific expression in polyploid organisms.
This package is part of the [LongPolyASE](https://polyase.readthedocs.io/en/latest/index.html) framework for long-read RNA-seq allele-specific expression analysis in polyploid organisms.
Please see [syntelogfinder](https://github.com/NIB-SI/syntelogfinder) and [longrnaseq](https://github.com/NIB-SI/longrnaseq) for generating the input data for polyase.

<img style="width: 30%;" alt="polyase_analysis" src="https://github.com/user-attachments/assets/a334a3a9-ac6f-403e-8d3e-a2f4b4bbbb6d" />

## Installation

PolyASE is avialble on [PyPI](https://pypi.org/project/polyase/).
You can install polyase using pip:

<pre><code>pip install polyase</code></pre>

Pyranges must be installed manually for reading GTF files.

To create a conda environemnt for running juypter notebook:

<pre><code>conda create -n polyase python=3.12 ipykernel pip && conda activate polyase && pip install polyase && pip install pyranges</code></pre>


## Tutorial

A tutorial for analysis of allele-sepecific gene and isoform expression in tetraploid potato can be found [here](https://polyase.readthedocs.io/en/latest/tutorial_potato.html)

The input data for the tutorial can be found [here](https://zenodo.org/records/17590760/files/polyase_tutorial_atlantic.zip?download=1&preview=1)


## Citation

