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.
PolyASE is avialble on PyPI. You can install polyase using pip:
pip install polyasePyranges 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 pyrangesA 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:1.3.3Then open http://localhost:8888 in your browser.
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.
-
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
-
Unzip the input data and place the notebook and all data files into a local
notebooks/folder. -
Start the container, mounting your
notebooks/folder:
docker run --rm -p 8888:8888 \
-v $(pwd)/notebooks:/home/user/notebooks \
nadjano/polyase:1.3.3- Open http://localhost:8888 in your browser, open
potato_polyase.ipynb, and update any file paths in the notebook to/home/user/notebooks/.
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