add mutational signature extraction script #48
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MatthijsPon
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The script extracts mutational signatures from VCFs, MAF and cbioportal studies. Also contains a dockerfile so dependencies are easily installed.
MatthijsPon
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inodb
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Mar 24, 2023
| # Needed to supress r-base region messages | ||
| ENV DEBIAN_FRONTEND=noninteractive | ||
| RUN apt install -y r-base r-cran-devtools libgsl-dev python3-pip wget | ||
| RUN Rscript -e "devtools::install_github('mskcc/temposig')" |
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prolly good if this is a specific version - or have some way to capture on datahub what version was run to generate the signature data
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@MatthijsPon this is pretty cool! Thanks for doing this! Will need to figure out on our end who could be a good person to review this |
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The script extracts mutational signatures from VCFs, MAF and cbioportal studies. Also contains a dockerfile in order to easily install dependencies.
This is the back-end implementation of RFC64.
Related front-end PR cBioPortal/cbioportal-frontend#4540 containing the front-end implementation.
Related datahub PR cBioPortal/datahub#1784 containing some studies with extracted mutational signatures