Difference between revisions of "Tutorials"
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These exercises run using a shared docker image, however the exercises are split into two separate notebooks. | These exercises run using a shared docker image, however the exercises are split into two separate notebooks. | ||
| − | * [ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC.pdf PLINK GWAS: Data QC Exercise] |
* PLINK GWAS: Data QC Exercise Output [PDF] | * PLINK GWAS: Data QC Exercise Output [PDF] | ||
| − | * [ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Substructure.pdf PLINK GWAS: Population Substructure Exercise] |
* PLINK GWAS: Population Substructure Output [PDF] | * PLINK GWAS: Population Substructure Output [PDF] | ||
* [https://hub.docker.com/r/statisticalgenetics/plink-gwas PLINK GWAS docker image] | * [https://hub.docker.com/r/statisticalgenetics/plink-gwas PLINK GWAS docker image] | ||
| − | * | + | * PLINK GWAS: Data QC Questions [PDF] |
| + | * PLINK GWAS: Data QC Answers [PDF] | ||
| + | * PLINK GWAS: Population Substructure Questions [PDF] | ||
| + | * PLINK GWAS: Population Substructure Answers [PDF] | ||
To pull and download the docker image from the Docker Hub repository, | To pull and download the docker image from the Docker Hub repository, | ||
Revision as of 14:31, 9 September 2026
Contents
- 1 Tutorials for Courses
- 2 Running Tutorials on Your Computer
- 3 FastLMM & GCTA
- 4 Mendelian Randomization
- 5 Pleiotropy
- 6 PLINK GWAS: Data Quality Control and Association Analysis Controlling for Population Substructure
- 7 Power Analysis
- 8 REGENIE
- 9 Regression and Intro to PLINK and R
- 10 Pencil and Paper Exercise
Tutorials for Courses
- FastLMM & GCTA
- Mendelian Randomization
- Pleiotropy
- PLINK GWAS: QC and Controlling for Population Substructure
- Power Analysis
- REGENIE
- Regression and Intro to PLINK and R
- Pencil and Paper Exercise
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
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 output [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 output [PDF]
- Mendelian Randomization docker image
- Mendelian Randomization questions [PDF]
- Mendelian Randomization answers [PDF]
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 output [PDF]
- Pleiotropy docker image
- Pleiotropy questions [PDF]
- Pleiotropy answers [PDF]
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
- PLINK GWAS: Data QC Exercise Output [PDF]
- PLINK GWAS: Population Substructure Exercise
- PLINK GWAS: Population Substructure Output [PDF]
- PLINK GWAS docker image
- PLINK GWAS: Data QC Questions [PDF]
- PLINK GWAS: Data QC Answers [PDF]
- PLINK GWAS: Population Substructure Questions [PDF]
- PLINK GWAS: Population Substructure Answers [PDF]
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
Power Analysis
REGENIE
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
