- A Galaxy tool for right censored failure time data.
- Provides Kaplan-Meier plots with confidence intervals, and optional Cox proportional hazards models
- Uses the lifelines package.
- Install to your Galaxy server from the toolshed - search for lifelines_km_cph_tool owned by fubar2
Runs Kaplan-Meier and generates a plot. Optional grouping variable race was supplied, so plots show confidence intervals
If 2 groups, runs a log-rank test for difference in the report.
If a comma separated list (for example: prio, age, race, mar, fin) of covariate column names is provided, a Cox proportional hazards model is run, the assumption of proportionality is tested, and recommendations made.
Partial plots for each covariate. Quintiles are used if there are >10 distinct values in the column. If you have non-ordinal covariates with >10 categores, this will produce garbage plots, but the model will also be hard to interpret so good luck.
Uses pandas read_csv with tabular delimiters so should work with any tabular data with the required columns - time and status for observations.
Issues to https://github.com/fubar2/lifelines_tool please. Autogenerated so pull requests are possibly meaningless but regeneration of a new version should work.
Tool made with the Galaxy ToolFactory: https://github.com/fubar2/galaxy_tf_overlay
Galaxy Training Network tutorials are available here
The generating history for this tool can be imported into a ToolFactory instance using this url: https://github.com/fubar2/lifelines_tool/raw/main/Galaxy-ToolFactory-History-lifelineskmcphtoolfactory.tar.gz
Once imported, switch to that new history. The original ToolFactory form can be recreated using the redo button. Editing the tool id will make a new tool, so all other edits to parameters can be made and the new tool generated without destroying the original sample.