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Table 1 Comparison of various features of the CancerSysDB with those of other cancer genomics data integration tools

From: Integrative analysis and machine learning on cancer genomics data using the Cancer Systems Biology Database (CancerSysDB)

  CancerSysDB TCGAbiolinks RTCGA cBio portal
GUI Web framework based on Groovy/Grails Based on Shiny None Web framework based on Spring Java
Query schema Hibernate R scripting R scripting SQL
Data upload Parametrized CSV file upload Direct access to GDC through API Data packages available on Bioconductor CSV files plus meta file
Query definition JSON-based Combination of R commands Combination of R commands REST-based API
Portability Native Docker implementation Hosted on Bioconductor Hosted on Bioconductor Hosted on GitHub
Programming skills required No Yes Yes No