polyase 1.3.5

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

Docker

A Docker image with PolyASE and JupyterLab is available on Docker Hub:

docker run --rm -p 8888:8888 \
  -v $(pwd)/notebooks:/home/user/notebooks \
  nadjano/polyase:1.3.3

Then open http://localhost:8888 in your browser.

Tutorial

A tutorial for analysis of allele-specific gene and isoform expression in tetraploid potato can be found here. The input data for the tutorial can be found here.

Running the tutorial within Docker

1. Download the tutorial notebook and input data:

   • Notebook (download the raw file): https://github.com/NIB-SI/polyase/blob/master/docs/source/potato_polyase.ipynb
   • Input data: https://zenodo.org/records/17590760/files/polyase_tutorial_atlantic.zip?download=1

2. Unzip the input data and place the notebook and all data files into a local notebooks/ folder.

3. Start the container, mounting your notebooks/ folder:

docker run --rm -p 8888:8888 \
  -v $(pwd)/notebooks:/home/user/notebooks \
  nadjano/polyase:1.3.3

4. Open http://localhost:8888 in your browser, open potato_polyase.ipynb, and update any file paths in the notebook to /home/user/notebooks/.

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

Citation