README.md

vitessce_suts

Setting up

1. Clone the repository:

    git clone https://github.com/karadavis-lab/suts_2024.git

2. Ensure you have Conda / Anaconda Installed, we recommend installing Miniforge.
3. cd into suts_2024 and create the conda environment with

    conda env create -f environment.yml

4. Activate the environment with conda activate suts

5. There are two notebooks which can be run in the scripts directory:

   1. process_fcs.ipynb if you would like to reproduce the data for vitessce.
   2. vitessce.ipynb is the notebook for running the visualization.

   Currently we recommend just running the vitessce notebook as the data is already preprocessed for ingestion.

6. Spline Visualization