Code to generate figures and analyses for Swarna et al. 2025.

Data to generate figures and analyese

Data to generate figures and analyses can be accessed at the following DOI: https://doi.org/10.5281/zenodo.17654220

📘 Environment Setup & Notebook Usage

This project uses a reproducible Conda environment defined in environment.yml. Follow the steps below to install the environment and run the notebooks.

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🔧 1. Install the Conda Environment

Make sure you have Anaconda or Miniconda installed.

Clone this repository:

git clone https://github.com/pachterlab/SBRGKLAYWMP_2025.git
cd SBRGKLAYWMP_2025

Create the environment from the YAML file:

conda env create -f environment.yml

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▶️ 2. Activate the Environment

conda activate swarna2025_env

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▶️ 3. Install wompwomp for alluvial plots

pip install git+https://github.com/pachterlab/wompywompy

🧠 4. Register the Jupyter Kernel

The ipykernel package is already included in the environment. Register this environment as a Jupyter kernel:

python -m ipykernel install --user --name swarna2025_env --display-name "Python (swarna2025_env)"

You will now see a new kernel inside Jupyter Notebook / JupyterLab.

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📓 5. Run the Notebooks

Launch Jupyter:

jupyter notebook

or

jupyter lab

Kernel → Change Kernel → Python (swarna2025_env)