I had to use GSEA for my own analysis (for multiple data sets) which led me to create docker image for fgsea R package for reproducible analyses. Details on how I created em cab be found at https://amnahsiddiqa.github.io/DockerJournal/
Download the test data (a .rnk file and a .gmt file ) from https://doi.org/10.6084/m9.figshare.13239512.v1
Run following
docker pull asidd13/base-r-fgsea
# -it for interactive ; -- rm tag is to remove conatiner afterwrads ; -v is volume mounting your homne directory holding input data (i.e. both gmt and rnk files) and where you want your results to be stored respectively.
docker run -it --rm -v path to data in your home directory:/Data -v path to directory where you want to store the results:/Output asidd13/base-r-fgsea:latest
Content type
Image
Digest
Size
723 MB
Last updated
almost 6 years ago
docker pull asidd13/base-r-fgsea