Tutorials

Tutorials for Courses

• FastLMM & GCTA | exercise [PDF] and docker image
• Mendelian Randomization | exercise [PDF] and docker image
• Pleiotropy | exercise [PDF] and docker image
• PLINK GWAS: QC and Controlling for Population Substructure | QC exercise [PDF], Substructure exercise [PDF], and docker image
• REGENIE | exercise [PDF] and docker image
• Regression and Intro to PLINK and R | Regression exercise [PDF], Intro to PLINK & R exercise[PDF], and docker image

Running Tutorials on Your Computer

We adopt docker to run our course material, and we have created various docker repositories with freely available Docker images for users to readily run our exercises on their own computers using Docker Desktop. These docker images are for multi-platform use (Mac, Windows, or Linux). More information regarding instructions to install Docker Desktop and to run the course material on your computer is detailed in the documentation below. 

General instructions

• Instructions to install Docker Desktop and running the course material on your computer

Tutorial specific instructions

Please refer to the previous section for instructions on the installation of Docker Desktop and basic usages. 

Material and instructions for specific exercise are listed in each section below. They provide links to pdf versions of the exercises and a minimal set of commands to use for downloading the docker images and running an exercise. 

FastLMM & GCTA

• FastLMM & GCTA exercise [PDF]
• FastLMM & GCTA docker image

To pull and download the docker image from the Docker Hub repository,

docker pull statisticalgenetics/fastlmm-gcta

To run the exercise from the downloaded docker image,

docker run --rm -p 8888:8888 statisticalgenetics/fastlmm-gcta

Mendelian Randomization

• Mendelian Randomization exercise [PDF]
• Mendelian Randomization docker image

To pull and download the docker image from the Docker Hub repository,

docker pull statisticalgenetics/mendelian-randomization

To run the exercise from the downloaded docker image,

docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization

Pleiotropy

• Pleiotropy Exercise [PDF]
• Pleiotropy docker image

To pull and download the docker image from the Docker Hub repository,

docker pull statisticalgenetics/pleiotropy

To run the exercise from the downloaded docker image,

docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy

PLINK GWAS: Data Quality Control and Association Analysis Controlling for Population Substructure

These exercises run using a shared docker image, however the exercises are split into two separate notebooks.

• PLINK GWAS: Data QC Exercise [PDF]
• PLINK GWAS: Population Substructure Exercise [PDF]
• PLINK GWAS docker image

To pull and download the docker image from the Docker Hub repository,

docker pull statisticalgenetics/plink-gwas

To run the exercise from the downloaded docker image,

docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas

REGENIE

• Regenie Exercise [PDF]
• Regenie docker image

To pull and download the docker image from the Docker Hub repository,

docker pull statisticalgenetics/regenie

To run the exercise from the downloaded docker image,

docker run --rm -p 8888:8888 statisticalgenetics/regenie

Regression and Intro to PLINK and R

These exercises run using a shared docker image, however the exercises are split into two separate notebooks.

• Regression exercise [PDF]
• Intro to PLINK & R Exercise [PDF]
• Regression and Intro to PLINK & R docker image

To pull and download the docker image from the Docker Hub repository,

docker pull statisticalgenetics/regression-plink-r

To run the exercise from the downloaded docker image,

docker run --rm -p 8888:8888 statisticalgenetics/regression-plink-r