Additional file 1: of Integrative analysis and machine learning on cancer genomics data using the Cancer Systems Biology Database (CancerSysDB)

The source code of the database queries and workflow scripts for the three use cases reported in the paper. The results can be reproduced using the query results and analysis scripts provided. File query1.csv contains the barcodes of all samples for which mutation data do exist. File query2.csv contains the barcodes of all samples which carry a mutation in the gene of interest. Finally, query3.csv contains the survival data (according to Fig. 1a), a list of all mutations of patients in the cohort of interest (according to Fig. 1b), or a list of all genomic segments with aberrant copy number in the cohort of interest (according to Fig. 1c). There are small discrepancies between the number of patients with mutation data and the number of patients with survival data (Fig. 1a) and copy number data (Fig. 1c). (ZIP 4981 kb)