EssenCDNA

A repository for identifying the correlation between gene essentiality and ecDNA presence in cell lines. The analysis notebook input filepaths can be changed to study any version of the corresponding DepMap essentiality data or Amplicon Architect ecDNA data.

Setup:

To set up the environment necessary to run the analysis notebook, follow these steps:

1. Install Conda: If you do not already have conda installed, you can download and install Miniconda here. Choose the appropriate installer for your operating system.
2. Create the conda environment: Once conda is installed, navigate to the project directory and create the environment using the provided environment.yml file. Run the following command:

conda env create -f environment.yml

3. Run the EssenCDNA.ipynb analysis notebook.

Results:

Results from the sample run of the notebook with the data found in the repository can be found here.