Provided here are the code and functions that we used to create each figure in our manuscript. All data are available on Single Cell Portal SCP2424.

1. Install Jupyter Notebook

   • You can download Jupyter here.
   • Instructions on running Jupyter notebooks are available here.

2. Download the Data

   • The dataset can be found at: Single Cell Portal SCP2424
   • Download all required files into a directory.

3. Install Required Packages

   • Create a Conda environment and install dependencies:
   conda create --name <env> --file environment.yml conda activate <env>

This Code Capsule is hosted on Code Ocean, a platform recommended for reproducible code.

This option runs all scripts and generates all figures, saving them in the results folder. It is the best option for verifying figure outputs efficiently.

1. Set the script to run:

   • Locate the file run under the code directory.
   • Right-click it and select "Set as File to Run".
   • (Optional: To run a specific figure, modify this file to comment out other figure commands.)

2. Start the Reproducible Run:

   • Click "Reproducible Run".
   • Main figures (Figs. 1–5) will take ~50 minutes to complete.
   • You may exit the window and return later to view the results.

3. Review the results:

   • Open the results folder to access:
     • All generated figures.
     • The executed Jupyter Notebook saved as an HTML file (with outputs for easy review).
   • Download results if needed before running supplementary figures.

4. Run Supplementary Figures (Optional):

   • Repeat steps 1–3, but this time, right click and set run_supp as the file to run.
   • Supplementary figures will take ~40 minutes to complete.

This method allows for step-by-step execution but may require restarting due to memory constraints.

1. Launch JupyterLab:

   • Under "Reproducible Run", click "Launch a Cloud Workstation" and select the JupyterLab icon.

2. Wait for Capsule Initialization:

   • The environment includes all necessary data, code, and dependencies and may take a few minutes to load.

3. Set Up the Environment:

   • Once loaded, execute the code in the “Set up environment” section.
   • (This step is required before running any analysis.)

4. Run Figure-Specific Code:

   • Open the notebook for the desired figure.
   • Go to Kernel > Restart Kernel and Run All Cells…
   • (Note: If the kernel dies due to memory limitations, re-run the "Set up environment" code before executing any figure-specific code again.)
   • You do not need to run previous figure scripts to execute a specific panel. (For example, you can run Fig. 4I independently without running Figs. 4F-H.)