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AML Multistage Reproducibility Study

This repository is forked from gerstung-lab/AML-multistage for our manuscript Validating the knowledge bank approach for personalized prediction of survival in acute myeloid leukemia: a reproducibility study.

Reproducibility assessment

/doc/SupplementaryMethodsCode.R is to present our modifications of the original code by Gerstung et al.. We modified the code in order to reproduce their published results in Gerstung M, Papaemmanuil E, Martincorena I, et al. Precision oncology for acute myeloid leukemia using a knowledge bank approach. Nat Genet. 2017;49(3):332-340. doi:10.1038/ng.3756.

For comparison purposes, modifications were only made when coding errors from the original R script prevented the continuation of the process.

Reanalysis

We tailored the source code and performed a reanalysis for ‘concept testing’ purposes: to clarify the conflation between causal inference and predictive model in the original paper. The results are summarized in Fig. 3 in our manuscript.

  • /reanalysis/Fig3.R is to generate Fig. 3, which works on the same data in /data as did in the original study.

  • In addition, we provided a Docker image for our reanalysis: https://hub.docker.com/repository/docker/yujunxu/aml-multistage-reanalysis (built from /reanalysis/Dockerfile and /reanalysis/install_packages.R, tested on Debian 11.0 64-bit and Ubuntu 18.04 64-bit)

    • docker pull
      docker pull yujunxu/aml-multistage-reanalysis:1.3
    • docker run
      docker run -it yujunxu/aml-multistage-reanalysis:1.3 /bin/bash

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