HOPE cohort analysis

Module authors: Komal S. Rathi, Zhuangzhuang Geng, Jo Lynne Rokita, Joseph M. Dybas

Clone the repository

To clone the repository, run:

git clone git@github.com:d3b-center/hope-cohort-analysis.git

Download the data

To download the current data release:

bash download-data.sh

Run the script on docker

To pull the docker image, run the command line:

docker pull pgc-images.sbgenomics.com/d3b-bixu/d3b_hope_analysis:latest

To start the docker container, run the command line below. For mac M1 user, add --platform=linux/arm64.

docker run -d -e PASSWORD=pass -p 8787:8787 --name <CONTAINER_NAME> -v $PWD:/home/rstudio/hope-cohort-analysis pgc-images.sbgenomics.com/d3b-bixu/d3b_hope_analysis:latest

To use docker in command line:

docker exec -ti <CONTAINER_NAME> bash

Navigate to the repository root

cd /home/rstudio/hope-cohort-analysis

Modules

analyses
├── alt-analysis
├── data-availability
├── master-annotation
├── merge-files
├── tp53_nf1_score
├── molecular-subtyping-HGG
├── msi-sensor-analysis
├── oncoplots
└── survival-analysis 

1) data-availability: This module has scripts to create data availability plots. 2) merge-files: This module has scripts to merge files obtained from cavatica i.e. RSEM gene expression, Consensus MAF, ControlFREEC, Fusions which are then filtered and annotated. 3) master-annotation: This module combines various sources of information from the HOPE group into one single tsv file for downstream analyses. 3) msi-sensor-analysis: Downstream analyses with MSISensor pro outputs. 4) oncoplots: This module has scripts to create oncoplots and cascade plots. Reference files and genelists were obtained from PNOC003 5) survival-analysis: This module has scripts to do survival analysis with ALT status and molecular subtypes. 6) alt-analysis: Downstream analyses with ALT status. 7) tmb-calculation: Adapted from OpenPedCan-anaysis