A R project for survival analysis

A R project for survival analysis based on the R survival package.

This project comes as a “template” which is available at https://github.com/auwerxlab/survival_analysis. It provides code for the analysis but no data.

Features

• Kaplan-Meier survival curves

• Cox proportional hazards regression model

• Compatibility with RENKU

• Integration with SLIMS

Intro

• What’s in this project

Setup

• Working locally
  • 1. Requirements
  • 2. Get the R project “template”
  • 3. Update the README file
  • 4. Install R packages
  • 5. Keep track of your work
  • 6. Keep up to date with the last version of the project “template”
• Working on RENKU
  • 1. Import the R project “template” into RENKU
  • 2. Build the working environment image
  • 3. Launch an Interactive Environment
  • 4. Install R packages
  • 5. Save your work !
  • 6. Keep up to date with the last version of the project “template”

Usage

• 1. Data collection and data format
  • Spreadsheet for Deads/Censored counts
    • templates/survival_data_collection.xlsx
• 2. Data analysis
  • R scripts
    • bin/build_survival_curves.R
  • R notebooks
    • notebooks/build_survival_curves.rmd
  • IPython notebooks
    • renku_simple_workflow.ipynb
    • auwerxlab_workflow.ipynb

Tutorial

• C. elegans drug response
  • Dataset
  • Analysis
  • Results