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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
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New tool requests (Kaplan-Meier plot & Cox-PH model) for survival analysis #5393

Open DariaKoppes opened 1 year ago

DariaKoppes commented 1 year ago

During my research I made a couple of Galaxy workflows for cancer survival prediction but was missing some functionalities that I think would be helpful for others as well if they could be added as new tools to Galaxy.

  1. There is no tool currently that supports the creation of Kaplan-Meier plots and showing the log rank p-value inside the plot. I noticed other Graphic tools are available that use the R package ggplot2. It would be great if the Kaplan-meier plot using the R function 'ggsurvplot' could be added as well.
  2. Also fitting a Cox proportional hazards (Cox-PH) model is not supported in Galaxy at the moment with its own tool. A Cox-PH model could be used to assess correlations between features and survival outcomes, utilizing it for further feature selection for example.

I know an interactive RStudio tool is available to perform these operations. However for usage in workflows and more ease of use in general I think adding separate tools is more beneficial.

fubar2 commented 1 year ago

@DariaKoppes - there's a new tool at https://github.com/fubar2/lifelines_tool ready for testing if you are able to get it installed in your own test server, any feedback would be very much welcomed. Python only - lifelines is very slick - the tool just does the things you mentioned, giving some plots and the text report.