skills.rest
Kang-chen
Kang-chenCOMMUNITY
Explore all skills by this author →
GitHub

tcga-survival-analysis

Analyze TCGA gene expression survival outcomes via cBioPortal API and lifelines.

1|Updated Jan 29, 2026
Search Tags:#survival-analysis#gene-expression#lifelines#tcga#kaplan-meier#cox-model#cbioportal
One-click install
npx skills add https://github.com/Kang-chen/cartabio-ide-config --skill tcga-survival-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tcga-survival-analysis
Source: https://github.com/Kang-chen/cartabio-ide-config/tree/main/skills/omics/skills/tcga-survival-analysis
Command: npx skills add https://github.com/Kang-chen/cartabio-ide-config --skill tcga-survival-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Perform survival analysis on TCGA cancer data by interfacing with the cBioPortal API and lifelines to uncover how gene expression relates to patient outcomes.

Core Features & Use Cases

  • Data retrieval from cBioPortal for expression and clinical data
  • Kaplan-Meier survival analysis and log-rank test
  • Cox proportional hazards modeling
  • Support for multiple TCGA studies (LUAD, LUSC, BRCA, COADREAD, etc.)
  • Visualization of survival curves and hazard ratios

Quick Start

Provide a TCGA gene of interest to generate Kaplan-Meier survival curves with Cox analysis.

Frequently Asked Questions about tcga-survival-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I perform survival analysis on TCGA gene expression data?▼

To perform TCGA survival analysis, retrieve clinical and expression data through the cBioPortal API, then use the lifelines library to generate Kaplan-Meier curves and Cox proportional hazards models.

Can I analyze TP53 or EGFR mutations across BRCA and LUAD cohorts?▼

Yes, you can evaluate genes like TP53, KRAS, and EGFR across multiple TCGA cohorts including BRCA, LUAD, LUSC, and COADREAD by querying the cBioPortal API for expression and clinical data.

How do I create Kaplan-Meier curves and run log-rank tests with lifelines?▼

Use the lifelines library to process retrieved TCGA clinical data, generating Kaplan-Meier survival curves and applying log-rank tests to compare survival differences between patient groups.

Do I need to install pandas and requests to run Cox proportional hazards models?▼

Yes, this analysis requires Python packages including pandas, requests, and lifelines, providing the environment setup, data retrieval, and modeling steps needed to generate hazard ratios.

What is the best way to assess how gene expression relates to patient outcomes?▼

The best way to assess gene expression impact on patient outcomes is by building Cox proportional hazards models using TCGA data retrieved via the cBioPortal API to calculate hazard ratios.

Related Skills

Explore More Data & Analytics Skills→
AradotsoAradotso
5

harvard-art-museum-etl-pipeline

Automates ETL pipeline fetching, cleaning, and loading Harvard Art Museums API data into Python-supported formats for visualization.

Official
Advanced
sencersoylusencersoylu

survival-analysis

Estimate survival curves, compare groups, and model hazards with Kaplan-Meier, log-rank, and Cox methods.

Community
Intermediate
SciMate-AISciMate-AI
1

cbioportal-database

Fetch genomic alteration data for a gene from the cBioPortal REST API.

Official
Intermediate
tondevreltondevrel
19

lifelines

Analyze right-censored time-to-event data with Kaplan-Meier curves and Cox regression.

Community
Advanced