polyase 1.3.3

A package for analyzing allele-specific expression in polyploid organisms

PolyASE

A Python package for analyzing allele-specific expression in polyploid organisms. This package is part of the LongPolyASE framework for long-read RNA-seq allele-specific expression analysis in polyploid organisms. Please see syntelogfinder and longrnaseq for generating the input data for polyase.

Installation

PolyASE is avialble on PyPI. You can install polyase using pip:

pip install polyase

Pyranges must be installed manually for reading GTF files (most of the analysis can be run without pyranges).

To create a conda environemnt for running juypter notebook:

conda create -n polyase python=3.12 ipykernel pip && conda activate polyase && pip install polyase && pip install pyranges

Troubleshooting

if you get an error installing polyase with pip for some dependencies, e.g.:

• pyranges (a known issue on mac and windows).
• Failed to build llvmlit and numba

conda install -c conda-forge numba
conda install -c bioconda pyranges

Tutorial

A tutorial for analysis of allele-sepecific gene and isoform expression in tetraploid potato can be found here

The input data for the tutorial can be found here

Citation