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Table 1 Comparison of network-based survival analysis tools

From: The `dnet’ approach promotes emerging research on cancer patient survival

  dnet jActiveModules Net-Cox Reactome FI HyperModules HotNet
Platform/Language R Cytoscape Matlaba Cytoscape Cytoscape Python
Operating Systems independent b Yes Yes Yes Yes Yes Linux/Unix
Supervised by clinical survival data Yes Yes Yes No Yesc Yes
Able to adjust for covariables d Yese Yese,f No No No No
Require sophisticated parameter setup No Yes Yes No No Yes
Advanced network visualisation Yes Yes No Yes Yes Yes
Downstream evolution analysis Yes No No No No No
With full documentations Yes Yes No Yes Yes Yes
  1. aNeeds commercial license.
  2. bWindows, Mac, Linux/Unix.
  3. cDoes not support Cox regression.
  4. dIncludes age, gender and tumour type that are required for cross-tumour survival analysis.
  5. eIt incorporates this functionality from the package `survival’.
  6. fCan be extended for this purpose as shown in Figure2.