Conda environment setup for PIASO

Prerequisites

• You need Jupyter Lab installed to run the tutorial notebooks.

Setting up the environment

1. Create a new conda environment with Python 3.9:

   conda create -n piaso_env python=3.9
   

2. Activate the environment:

   conda activate piaso_env
   

3. Install scanpy using conda:

   conda install -c conda-forge scanpy
   

4. Install PIASO tools using pip:

   pip install piaso-tools
   

5. Install scrublet for cell filtering:

   pip install scrublet
   

6. Install louvain for community detection:

   pip install louvain
   

7. Install leidenalg version 0.10.2 for clustering:

   conda install -c conda-forge leidenalg=0.10.2
   

8. Install ipykernel to use this environment with Jupyter notebooks:

   conda install -c anaconda ipykernel
   

9. Add the environment to the Jupyter kernel list:

   python -m ipykernel install --user --name=piaso_env
   

Running the Tutorials

1. Open any tutorial notebook in Jupyter Lab.

2. Select piaso_env from the kernel dropdown in the top right corner.

3. Now you can run all cells in the notebook.

Your environment is now successfully set up to run all the PIASO tutorials.