Matchmaking from Molecular Oncology Almanac

Template repository to perform profile-to-profile matchmaking.

Matchmaking is a framework to identify genomically similar molecular profiles and evaluate that similarity profile based on shared labels, such as drug sensitivity. This repository contains data for cancer cell lines as represented in the present study, and can be revised to perform matchmaking on other cohorts.

Documentation detailing how to use code within this repository can be found in the matchmaking/ folder.

Installation

Download

This repository can be downloaded through GitHub by either using the website or terminal. To download on the website, navigate to the top of this page, click the green Clone or download button, and select Download ZIP to download this repository in a compressed format. To install using GitHub on terminal, type

git clone https://github.com/vanallenlab/moalmanac-matchmaking.git
cd moalmanac-matchmaking

Python dependencies

This repository uses Python 3.9. We recommend using a virtual environment and running Python with either Anaconda or Miniconda.

Run the following from this repository's directory to create a virtual environment and install dependencies with Anaconda or Miniconda,

conda create -y -n matchmaking python=3.9
conda activate matchmaking
pip install -r requirements.txt

Or, if using base Python,

virtualenv venv
source activate venv/bin/activate
pip install -r requirements.txt

To make the virtual environment available to jupyter notebooks, execute the following code while the virtual environment is activated,

ipython kernel install --user --name=matchmaking

Citation

Please cite our paper if using any information or code from this repository

Reardon, B., Moore, N.D., Moore, N.S., et al. Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. Nat Cancer (2021). https://doi.org/10.1038/s43018-021-00243-3

A protocol has also been published to accompany the above study, detailing how matchmaking is performed,

Reardon, B. & Van Allen, E. M. Molecular profile to cancer cell line matchmaking. Protocol Exchange https://doi.org/10.21203/rs.3.pex-1539/v1 (2021).