Polyase tutorial ================ Allelic gene and isoform expression analysis in potato ---------------------------------------------------------------- The jupyter notebook tutorial demonstrates how to use the **polyase** package to analyze allele-specific expression (ASE) in tetraploid potato using long-read RNA-seq data. The tutorial covers loading the data, calculating allelic ratios, filtering, statistical analysis, and visualization of ASE patterns. The notebook is available `here `_. Files necessary for this tutorial are deposited on Zenodo `here `_. Running the tutorial locally ----------------------------- Create a conda environment that also includes ipykernel to run jupyter notebooks: .. code-block:: bash conda create -n polyase python=3.12 ipykernel pip && conda activate polyase && pip install polyase && pip install pyranges If you get an error regarding the installation of pyranges (a known issue on mac and windows), then try to install it via conda: .. code-block:: bash conda install -c bioconda pyranges Running the tutorial within Docker ------------------------------------ A Docker image with PolyASE and JupyterLab is available on `Docker Hub `_. 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: .. code-block:: bash 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/``. .. raw:: html :file: _static/potato_polyase.html