Module authors: Komal S. Rathi, Zhuangzhuang Geng, Jo Lynne Rokita, Joseph M. Dybas
To clone the repository, run:
git clone git@github.com:d3b-center/hope-cohort-analysis.git
To download the current data release:
bash download-data.sh
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
cd /home/rstudio/hope-cohort-analysis
analyses
├── alt-analysis
├── data-availability
├── master-annotation
├── merge-files
├── tp53_nf1_score
├── molecular-subtyping-HGG
├── msi-sensor-analysis
├── oncoplots
└── survival-analysis
data-availability
: This module has scripts to create data availability plots.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.master-annotation
: This module combines various sources of information from the HOPE group into one single tsv file for downstream analyses.msi-sensor-analysis
: Downstream analyses with MSISensor pro outputs.oncoplots
: This module has scripts to create oncoplots and cascade plots. Reference files and genelists were obtained from PNOC003survival-analysis
: This module has scripts to do survival analysis with ALT status and molecular subtypes.alt-analysis
: Downstream analyses with ALT status.tmb-calculation
: Adapted from OpenPedCan-anaysis