This is a repository for reproducing the analysis in the paper: Gene regulatory network integration with multi-omics data enhances survival predictions in cancer . We recommend cloning this repository and then downloading and unzipping all the data in the cloned repository directory.
All data used can be found on Zenodo. We also provide a container with the environment used for this analysis for reproducibility, which is also available on Zenodo along with instructions for using it.
The code used to download the raw data can be found in the download_data subdirectory along with a more detailed README.
The PANDA-LIIONESS networks can be reproduced using the workflow found in the single_sample_networks.ipynb jupyter notebbok. See the README in the notebooks subdirectory of this repository.
The remainder of the analysis is documented in the notebook JDR_net.ipynb found in the notebooks subdirectory. Some intermediate files are provided on Zenodo to reduce run-time. These are:
- the factorisations
- the indegrees & outdegrees of the single sample networks.
Most of the analysis detailed in JDR_net.ipynb was performed with the MARMOT tool, which can be found in the repository below:
https://github.com/rtpop/MARMOT