An initial descriptive analysis of AACR's GENIE BPC bladder cancer cohort. This repo contains only the analysis portions completed by Sage Bionetworks (originally Alex Paynter).
To clone this repository, run the following in the command line from a machine with git installed:
git clone https://github.com/Sage-Bionetworks/genie-bpc-bladder-landscape-manu
This repository:
- Was tested and run on R version 4.4.2.
- Uses R projects. When running any codes, please open the
.RProjfile first. - Does not use
renvto manage package environments. - Does not use
dockeror other containerization to manage deployment.
The code may work without appreciation of these tools, but no guarantees.
To run the code in this respository you will need:
- A Synapse account which has download rights for GENIE data. See below on data versions.
- The synapser R package, which will also require a python installation (follow instructions at that link).
- Note: This is only used to acquire the data. It is technically possible to download the data by pointing and clicking if you want to.
The top-level workflow of the project is in main.R. This calls the other analysis scripts in the correct sequence to reproduce my workflow. Other top level folders include:
/analysis- Scripts (analysis/scripts), quarto/rmarkdown files (analysis/reports) and any other analysis code excluding function definitions./data-raw- Raw data, where raw means "as it comes in the data release."/data- Processed data, saved at various stages in the analysis./output- Figures, rendered reports, tables, etc./R- Function definitions. These are sometimes written with {roxygen}-style documentation like a package would be.
We use GENIE BPC Bladder release version 1.1, which is only available to GENIE consortium members. It should have high similarity with the forthcoming 2.0-public release, expected here sometime in the future.
If you are not a consortium member and you want to access the exact data version to reproduce this analysis, please send a request explaining this to [email protected].
The structure, processing and flow of data is described in detail in the PDF data guide, which accompanies the data files.
We wish to thank the following groups for their upstream contributions to the data:
- AACR Project GENIE team
- Sage bionetworks GENIE team - processing and releases.
- MSKCC biostatistics team
- The patients and institutions who contributed data to the GENIE and GENIE BPC registries.
The license for this material is GNU GPLv3. That means you can use this code, as long as your code remains open for others to use. We're on a strict honor system with no repercussions here so thanks in advance for definitely following this.
If you have additional questions please write [email protected]. If that fails, try [email protected] and ask them to put you in touch with me.