The code reproduces mRNA-based stemness indices (mRNAsi) from "Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation" by Malta, Sokolov, et al.
Prerequisites:
- Install Docker
- Sign up for a synapse.org account and ensure that you have access to:
- syn2701943 - normalized mRNA data from PCBC (used to learn the stemness signature)
- syn4976369 - normalized and batch-corrected PanCan33 data
Download all relevant data with
docker run --rm -v "$PWD":/data artemsokolovdh/pancanstem /app/get-data.R <Synapse Username> '<Synapse Password>'
where
--rmwill clean up the container after it finishes running-v "$PWD":/datamakes the current working directory to be/data/inside the containerartemsokolovdh/pancanstemis the container, currently hosted on DockerHub- The source code of
/app/get-data.Rcan be found in this GitHub repo - Important:
<Synapse Password>must be enclosed by quotes to ensure that special characters are handled properly
Once the script finishes, you will find two folders, PCBC and PanCan33, containing downloaded data. From here, the stemness signature and indices can be generated by running
docker run --rm -v "$PWD":/data artemsokolovdh/pancanstem /app/main.R