2022 Summer Institute - Supplemental Materials

Preparing for Big Data in Biomedical Research

These three software programs will be used throughout the course. These programs are free and should be downloaded prior to August 1:

In addition, these online tools will be used. Please bookmark them in advance:

If you have little or no experience in R and Linux, please review these materials prior to the start of the course:

Participants who would like a primer on biomedical terminology are encouraged to consult the Beginner’s Guide to RNA-seq or similar resources.

 

Preparing for Introduction to Causal Inference

We will be using R software for demonstrations, activities, and (optional) homework.

For a free, gentle introduction to many causal inference concepts, you may wish to consult an online book authored by Miguel Hernán and Jamie Robins. 

 

Preparing for Regression and Modeling in R

Before the course starts, students not already familiar with R should practice data importing and simple programming with R and RStudio (both available as free downloads).

An introduction to R that many previous students found helpful can be found at https://cran.r-project.org/doc/manuals/r-release/R-intro.pdf (Venables, Smith, and the R Core Team). See also DataCamp's Quick-R tutorial and Frank E. Harrell Jr.'s Regression Modeling Strategies: With Applications to Linear Models, Logistic Regression, and Survival Analysis.

 

Preparing for Cloud Computing and Case Studies in Biomedical Data Science

The following three software programs will be used throughout the duration of the course.  These programs are free and should be downloaded prior to the start date:

  • R:  cran.r-project.org/
  • Python:  www.python.org/
  • Visual Studio Code: code.visualstudio.com/
     

The following resources will also be accessed during this course: 

  • WDL: github.com/openwdl/wdl
  • Cromwell: github.com/broadinstitute/cromwell
  • Summer Institute 2022 Cloud Computing Workspace: rstudio.tbilab.org
  • UK Biobank: www.ukbiobank.ac.uk 
  • UK Biobank RAP: ukbiobank.dnanexus.com/landing
  • All of Us: allofus.nih.gov