uveal-melanoma

Bakhoum MF*, Francis JH*, Agustinus A, Earlie EM, Di Bona M, Abramson DH, Duran M, Masilionis I, Molina E, Shoushtari AN, Goldbaum MH, Mischel PS, Bakhoum SF, Laughney AM. Loss of Polycomb Repressive Complex 1 activity and chromosomal instability drive uveal melanoma progression. Nature Communications 12, 5402 (2021). https://doi.org/10.1038/s41467-021-25529-z

* Authors contributed equally to this study.

Data Access: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE160883

Lab Website: https://laughneylab.com/

Overview

The uveal-melanoma repository contains the code used for the single cell data analysis of the tumor cell subpopulations for the uveal melanoma study. This analysis includes 6 primary tumor samples from patients at MSK, along with an independent cohort of 8 primary tumor samples from Durante et al. A brief analysis was also performed on the reference cohort of 80 primary uveal melanoma sample from the TCGA study.

Dependencies

uvmel_tumorcells_v4.ipynb:

1. Python 3
2. Jupyter Notebooks
3. R-4.0.2
4. R for Juypter Notebooks
5. Docker
6. The uvmel Docker image

Guide

The uvmel_tumorcells_v4.ipynb notebook is the Python notebook used for the main single-cell analyses and figure generation. This notebook can be run within a container spun from the uvmel Docker image. For help starting a container based on this docker image, please reference the docker documentation.

The following commands will install the uvmel docker image and the github repository.

docker pull ghcr.io/laughneylab/uveal-melanoma/uvmel:latest

git clone https://github.com/LaughneyLab/uveal-melanoma.git