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add survival and collapsed life table outputs suggested by Wolfgang
author fubar
date Thu, 10 Aug 2023 22:52:45 +0000
parents 232b874046a7
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1 # lifelines_tool - lifelines statistical package wrapped as a Galaxy tool. 1 # lifelines_tool - lifelines statistical package wrapped as a Galaxy tool.
2 2
3 ## Galaxy tool to run failure time models using lifelines 3 A Galaxy tool for right censored failure time data.
4 4
5 ## Install to your Galaxy server from the toolshed - search for lifelines_km_cph_tool owned by fubar2 5 Provides Kaplan-Meier plots with confidence intervals, and optional Cox proportional hazards models
6 6
7 ### More at https://lazarus.name/demo/ 7 Uses the [lifelines](https://lifelines.readthedocs.io/en/latest/index.html) package.
8 8
9 #### Using the Rossi sample input data from lifelines, tool outputs include: 9 ### Install to your Galaxy server from the toolshed - search for lifelines_km_cph_tool owned by fubar2
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11 More at https://lazarus.name/demo/
12
13 #### Using the Rossi sample recidivism data from lifelines:
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15 Runs Kaplan-Meier and generates a plot. Optional grouping variable.
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17 Plots show confidence intervals
10 18
11 ![KM plot sample](lifelines_rossi_km.png) 19 ![KM plot sample](lifelines_rossi_km.png)
12 and 20
13 ![KM plot sample](lifelines_rossi_schoenfeld.png) 21 If 2 groups, runs a log-rank test for difference.
14 and 22
15 ![KM plot sample](lifelines_report.png) 23 ![KM plot sample](lifelines_report.png)
16 24
25 If a comma separated list (for example: prio, age, race, mar, fin) of covariate column names is provided,
26 a Cox proportional hazards model is run, the assumption of proportionality is tested, and
27 recommendations made.
28 ![KM plot sample](lifelines_rossi_schoenfeld.png)
17 29
18 Runs Kaplan-Meier and generates a plot. Optional grouping variable. 30 Also included are partial plots for each covariate like these from the Rossi recidivism lifelines sample data
19 If 2 groups, runs a log-rank test for difference. 31 used in the tool test.
20 Plots show confidence intervals
21 32
22 If a list of covariate column names is provided, these are used in a 33 ![C-PH partial plot samples](agepartialrossi.png)
23 Cox Proportional Hazards model with tests for proportionality.
24 34
25 Should work with any tabular data with the required columns - time and status for observations. 35 ![C-PH partial plot samples](parolepartialrossi.png)
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37 Uses pandas read_csv with tabular delimiters so should work with any tabular data with the required columns - time and status for observations.
26 38
27 Issues to https://github.com/fubar2/lifelines_tool please. 39 Issues to https://github.com/fubar2/lifelines_tool please.
28 Autogenerated so pull requests are possibly meaningless but regeneration of a new version should work. 40 Autogenerated so pull requests are possibly meaningless but regeneration of a new version should work.
29 41
30 ## Tool made with the Galaxy ToolFactory: https://github.com/fubar2/galaxy_tf_overlay 42 ## Tool made with the Galaxy ToolFactory: https://github.com/fubar2/galaxy_tf_overlay