Tumor evolution across multiple time points in OpenPBTA patients

This repository is no longer maintained.

To reproduce the code in this repository:

This repository contains a docker image and code used to conduct analyses for the manuscript noted above.

1. Clone the repository

git clone https://github.com/d3b-center/pbta-tumor-evolution.git

2. Pull the docker container:

docker pull pgc-images.sbgenomics.com/antoniachroni/pbta-tumor-evolution:latest

3. Start the docker container, from the pbta-tumor-evolution folder, run:

docker run --platform=linux/amd64 --name <CONTAINER_NAME> -d -e PASSWORD=ANYTHING -p 8787:8787 -v $PWD:/home/rstudio/pbta-tumor-evolution pgc-images.sbgenomics.com/antoniachroni/pbta-tumor-evolution:latest

4. To execute shell within the docker image, from the pbta-tumor-evolution folder, run:

docker exec -ti <CONTAINER_NAME> bash

5. Run the download-data.sh shell script to obtain latest data files:

bash download-data.sh

6. Navigate to an analysis module and run the shell script:

cd /home/rstudio/pbta-tumor-evolution/analyses/module_of_interest

Below is the main directory structure listing the analyses and data files used in this repository

.
├── analyses
   └── sample-distribution-analysis
├── data
    ├── gencode.v39.primary_assembly.annotation.gtf.gz
    └── v1
       ├── gene-counts-rsem-expected_count-collapsed.rds
       ├── gene-expression-rsem-tpm-collapsed.rds
       ├── histologies.tsv
       ├── md5sum.txt
       ├── release-notes.md
       └── snv-consensus-plus-hotspots.maf.tsv.gz
├── Dockerfile
├── download-data.sh
├── LICENSE
├── README.md
└── scripts
    ├── install_bioc.r
    └── install_github.r

Code Authors

Jo Lynne Rokita (@jharenza) and Antonia Chroni (@AntoniaChroni)

Contact

For questions, please submit an issue in https://github.com/rokitalab/tumor-evolution.