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Lifelines kaplan meier starter

Skill ma-compbio-lab/SkillFoundry/skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.From the repository description

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill lifelines-kaplan-meier-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

One thing to look at

  • runs commandsInstructs the agent to run 3 commands, including `slurm/envs/statistics/bin/python skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter/scripts/run_lifelines_kaplan_meier.py` and 2 more.

SKILL.md

1.2 KB, 307 tokens by cl100k_base, as published. Nobody here has run it

Lifelines Kaplan Meier Starter

Use this skill to run a deterministic Kaplan-Meier survival analysis over a toy cohort and summarize per-group survival curves.

What it does

  • Loads a tiny cohort table with durations, events, and group labels.
  • Fits one Kaplan-Meier curve per group with lifelines.
  • Returns compact JSON with median survival times and survival probabilities at fixed time points.
  • Optionally renders a PNG survival plot.

When to use it

  • You need a local starter for survival-analysis workflows.
  • You want a verified template for grouped time-to-event data in Python.

Example

slurm/envs/statistics/bin/python skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter/scripts/run_lifelines_kaplan_meier.py \
  --input skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter/examples/toy_survival_cohort.tsv \
  --summary-out scratch/lifelines/kaplan_meier_summary.json \
  --png-out scratch/lifelines/kaplan_meier_plot.png

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/clinical-biomedical-data-science/lifelines-kaplan-meier-starter/tests -p 'test_*.py'
  • Repository smoke: python3 -m unittest tests.smoke.test_phase25_agent_and_clinical_skills -v

What ships with it: 7 files

7.5 KB alongside SKILL.md, 2 of them executable

assets/

examples/

scripts/

tests/

Keep looking

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