Histolab Whole Slide Image Tiling
davila7/claude-code-templates
Processes digital pathology whole slide images with histolab: tissue detection, mask creation, tile extraction and dataset preparation for deep learning.
Complete survival analysis library in Python. An agent skill from brycewang-stanford/Auto-Empirical-Research-Skills.
Install Lifelines
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill lifelines -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills lifelines --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/63-tondevrel-scientific-agent-skills/lifelines .claude/skills/lifelines && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "lifelines" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/63-tondevrel-scientific-agent-skills/lifelines into .claude/skills/lifelines/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lifelines", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/63-tondevrel-scientific-agent-skills/lifelinesType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill lifelines -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills lifelines --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/63-tondevrel-scientific-agent-skills/lifelines .agents/skills/lifelines && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "lifelines" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/63-tondevrel-scientific-agent-skills/lifelines into .agents/skills/lifelines/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lifelines", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill lifelines -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills lifelines --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/63-tondevrel-scientific-agent-skills/lifelines .cursor/skills/lifelines && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "lifelines" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/63-tondevrel-scientific-agent-skills/lifelines into .cursor/skills/lifelines/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lifelines", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git --path skills/63-tondevrel-scientific-agent-skills/lifelines--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill lifelines -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills lifelines --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/63-tondevrel-scientific-agent-skills/lifelines .gemini/skills/lifelines && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "lifelines" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/63-tondevrel-scientific-agent-skills/lifelines into .gemini/skills/lifelines/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lifelines", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills lifelinesInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill lifelines -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/63-tondevrel-scientific-agent-skills/lifelines .github/skills/lifelines && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "lifelines" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/63-tondevrel-scientific-agent-skills/lifelines into .github/skills/lifelines/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lifelines", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill lifelines -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills lifelines --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/63-tondevrel-scientific-agent-skills/lifelines .opencode/skills/lifelines && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "lifelines" agent skill from https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/main/skills/63-tondevrel-scientific-agent-skills/lifelines into .opencode/skills/lifelines/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "lifelines", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
lifelines- GitHub stars
- 4.5k
- Token cost
- ~771 tokens
- SKILL.md length
- 220 words
- Files
- 1
- Skills in repo
- 383
- Repo updated
- First seen
- Licence
- MIT
At a glance
Complete survival analysis library in Python. An agent skill from brycewang-stanford/Auto-Empirical-Research-Skills.
- Tasks that involve Clinical and healthcare research
- SKILL.md covers When to Use, Core Principles, Quick Reference and Critical Rules, plus 1 more section
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Lifelines is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Complete survival analysis library in Python. Handles right-censored data, Kaplan-Meier curves, and Cox regression. Standard for clinical trial analysis and epidemiology.
Its SKILL.md is about 770 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Clinical and healthcare research. It works with Python. The repository describes itself as: 🔬 A curated collection of 23,000+ agent skills for empirical research across 8 social science disciplines. | 精选 23,000+ AI Agent 技能库，覆盖8大社会科学学科的实证研究。CoPaper.AI… The licence is MIT.
When your agent uses it
- Tasks that involve Clinical and healthcare research
Example prompts
- “/lifelines”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit 9fa87d8. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Lifelines loads about 771 tokens when it runs. Until then it costs about 45 tokens; SKILL.md has 220 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from brycewang-stanford/Auto-Empirical-Research-Skills at commit 9fa87d8, republished under its MIT licence (© brycewang-stanford). 220 words, ~771 tokens.
Download SKILL.mdSave it as
.claude/skills/lifelines/SKILL.md (or your agent's skills folder).- name
- lifelines
- description
- Complete survival analysis library in Python. Handles right-censored data, Kaplan-Meier curves, and Cox regression. Standard for clinical trial analysis and epidemiology.
- version
- 0.28
- license
- MIT
Lifelines - Survival Analysis
In medicine, we often care about "Time to Event" (death, recovery, relapse). Lifelines handles the complexity of "censored" data (patients who left the study).
When to Use
- Analyzing clinical trial data (time to death, disease progression).
- Comparing survival between treatment groups.
- Identifying risk factors using Cox Proportional Hazards regression.
- Building survival models for prognosis.
- Epidemiology studies (time to infection, recovery).
Core Principles
Censoring
Patients who haven't experienced the event by the end of the study are "censored". Lifelines properly accounts for this.
Hazard Ratios
In Cox regression, a hazard ratio > 1 means increased risk; < 1 means decreased risk.
Survival Curves
Kaplan-Meier estimates the probability of survival over time without assuming a distribution.
Quick Reference
Standard Imports
from lifelines import KaplanMeierFitter, CoxPHFitter
from lifelines.statistics import logrank_test
import pandas as pdBasic Patterns
# 1. Kaplan-Meier (Visualizing survival)
kmf = KaplanMeierFitter()
kmf.fit(durations=df['days'], event_observed=df['died'])
kmf.plot_survival_function()
kmf.median_survival_time_ # Time when 50% have died
# 2. Cox Proportional Hazards (Risk factors)
cph = CoxPHFitter()
cph.fit(df, duration_col='days', event_col='died')
cph.print_summary() # See hazard ratios for age, drug type, etc.
cph.plot_partial_effects_on_outcome(covariates=['age'], values=[30, 50, 70])Critical Rules
✅ DO
- Use event_observed correctly - 1 = event occurred, 0 = censored.
- Check proportional hazards assumption - Use
cph.check_assumptions()to validate Cox model. - Compare groups with logrank test - Statistical test for survival curve differences.
- Plot confidence intervals - Survival estimates have uncertainty, especially with small samples.
❌ DON'T
- Don't ignore censoring - Treating censored patients as "survived" biases results.
- Don't use regular regression - Time-to-event data requires specialized methods.
- Don't assume proportional hazards - If violated, use stratified Cox or parametric models.
Advanced Patterns
Comparing Multiple Groups
from lifelines.statistics import multivariate_logrank_test
# Compare survival across treatment groups
results = multivariate_logrank_test(df['days'], df['group'], df['died'])
print(results.p_value)Parametric Models
from lifelines import WeibullFitter, ExponentialFitter
# When you need to extrapolate beyond observed data
wf = WeibullFitter()
wf.fit(df['days'], df['died'])
wf.plot()Lifelines transforms complex survival data into actionable medical insights, enabling evidence-based decisions in clinical research and practice.
© brycewang-stanford, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/63-tondevrel-scientific-agent-skills/lifelines of brycewang-stanford/Auto-Empirical-Research-Skills.
Open the folder on GitHubat commit 9fa87d8
Compare with similar skills
Lifelines next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Lifelines this skillbrycewang-stanford/Auto-Empirical-Research-Skills | 4.5k | — | ~771 | Automated safety check: Pass | MIT | |
| Histolab Whole Slide Image Tilingdavila7/claude-code-templates | 32k | 11 repos | ~5.1k | Automated safety check: Pass | MIT | |
| NeuroKit2 Biosignal Processingdavila7/claude-code-templates | 32k | 11 repos | ~3k | Automated safety check: Pass | MIT | |
| PyHealth Clinical ML Toolkitdavila7/claude-code-templates | 32k | 11 repos | ~4.4k | Automated safety check: Pass | MIT | |
| pydicom DICOM Toolkitdavila7/claude-code-templates | 32k | 11 repos | ~3.3k | Automated safety check: Pass | MIT | |
| openFDA Regulatory Data Queriesdavila7/claude-code-templates | 32k | 11 repos | ~3.6k | Automated safety check: Pass | MIT |
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Builds machine learning pipelines on clinical data with PyHealth: EHR datasets, prediction tasks, medical code mapping, healthcare models and evaluation.
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Reads, edits, anonymizes and converts DICOM medical imaging files with pydicom, including pixel data extraction and compressed transfer syntaxes.
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Queries the openFDA API from Python for drug, device, food and veterinary data: adverse events, recalls, labels, approvals, NDC and UNII lookups.
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Searches and reads biomedical papers, FDA/PMDA/EMA documents, clinical trials, and protein records with the GXL Paperclip CLI and Python SDK.
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Related
Works with
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Questions about Lifelines
What does Lifelines do?
Complete survival analysis library in Python. An agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Lifelines is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Complete survival analysis library in Python.
When should I use Lifelines?
Lifelines fits situations like: tasks that involve Clinical and healthcare research.
How do I install Lifelines in Claude Code?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill lifelines -a claude-code`. Or copy the skill folder (skills/63-tondevrel-scientific-agent-skills/lifelines in brycewang-stanford/Auto-Empirical-Research-Skills) into .claude/skills/lifelines in your project. Claude Code loads it when a task matches its description.
How do I install Lifelines in Codex?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill lifelines -a codex`. Or copy the skill folder (skills/63-tondevrel-scientific-agent-skills/lifelines in brycewang-stanford/Auto-Empirical-Research-Skills) into .agents/skills/lifelines in your project. Codex loads it when a task matches its description.
Can I use Lifelines in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill lifelines -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/lifelines, .gemini/skills/lifelines, .github/skills/lifelines and .opencode/skills/lifelines in your project.
What does Lifelines need to run?
SKILL.md names no scripts, command-line tools or credentials: Lifelines is instructions for the agent only. Our summary lists: Python 3.
Does Lifelines access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Lifelines safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Lifelines use?
Lifelines is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Lifelines use?
About 771 tokens (SKILL.md is roughly 3.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Lifelines?
Skills that share tags, products or a category with Lifelines: Histolab Whole Slide Image Tiling (davila7/claude-code-templates, 32k stars), NeuroKit2 Biosignal Processing (davila7/claude-code-templates, 32k stars), PyHealth Clinical ML Toolkit (davila7/claude-code-templates, 32k stars) and pydicom DICOM Toolkit (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Lifelines?
brycewang-stanford (a GitHub user) maintains it in brycewang-stanford/Auto-Empirical-Research-Skills, which has 4,542 GitHub stars. The repository holds 383 skills in this directory. The repository was last updated on October 5, 2026.
Source: brycewang-stanford/Auto-Empirical-Research-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.