Difference between revisions of "Tutorials"
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==Tutorials for Courses== | ==Tutorials for Courses== | ||
| − | * [[Tutorials#FastLMM_&_GCTA|FastLMM & GCTA]] | + | * [[Tutorials#FastLMM_&_GCTA|FastLMM & GCTA]] |
| − | * [[Tutorials#Mendelian Randomization|Mendelian Randomization]] | + | * [[Tutorials#Mendelian Randomization|Mendelian Randomization]] |
| − | * [[Tutorials#Pleiotropy|Pleiotropy]] | + | * [[Tutorials#Pleiotropy|Pleiotropy]] |
| − | * [[Tutorials#PLINK_GWAS:_Data_Quality_Control_and Association_Analysis_Controlling_for_Population_Substructure|PLINK GWAS: QC and Controlling for Population Substructure]] | + | * [[Tutorials#PLINK_GWAS:_Data_Quality_Control_and Association_Analysis_Controlling_for_Population_Substructure|PLINK GWAS: QC and Controlling for Population Substructure]] |
| − | * [[Tutorials#REGENIE|REGENIE] | + | * [[Tutorials#Power_Analysis|Power Analysis]] |
| − | * [[Tutorials# | + | * [[Tutorials#REGENIE|REGENIE]] |
| + | * [[Tutorials#Regression_and_Intro_to_PLINK_and_R|Regression and Intro to PLINK and R]] | ||
| + | * [[Tutorials#Pencil_and_Paper_Exercise|Pencil and Paper Exercise]] | ||
==Running Tutorials on Your Computer== | ==Running Tutorials on Your Computer== | ||
| Line 11: | Line 13: | ||
===General instructions=== | ===General instructions=== | ||
| − | * [ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Statistical_Genetics_Exercise_Instructions.pdf Instructions to install Docker Desktop and running the course material on your computer] |
===Tutorial specific instructions=== | ===Tutorial specific instructions=== | ||
| Line 19: | Line 21: | ||
==FastLMM & GCTA== | ==FastLMM & GCTA== | ||
| − | * [ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/FastLMM_GCTA.pdf FastLMM & GCTA Exercise [PDF]] |
| − | * [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta FastLMM & GCTA | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/FastLMM_GCTA_Outputs.pdf FastLMM & GCTA Output [PDF]] |
| + | * [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta FastLMM & GCTA Docker Image] | ||
To pull and download the docker image from the Docker Hub repository, | To pull and download the docker image from the Docker Hub repository, | ||
| Line 30: | Line 33: | ||
==Mendelian Randomization== | ==Mendelian Randomization== | ||
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization.pdf Mendelian Randomization Exercise [PDF]] |
| − | * Mendelian | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization_Outputs.pdf// Mendelian Randomization Output [PDF]] |
| + | * [https://hub.docker.com/r/statisticalgenetics/mendelian-randomization Mendelian Randomization Docker Image] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization_Questions.pdf Mendelian Randomization Questions [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization_Answers.pdf Mendelian Randomization 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, | ||
| Line 41: | Line 47: | ||
==Pleiotropy== | ==Pleiotropy== | ||
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy.pdf Pleiotropy Exercise [PDF]] |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Outputs.pdf Pleiotropy Output [PDF]] |
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Docker Image] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Questions.pdf Pleiotropy Questions [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Answers.pdf Pleiotropy 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, | ||
| Line 54: | Line 63: | ||
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 [PDF]] |
| − | * [[ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Outputs.pdf PLINK GWAS: Data QC Output [PDF]] |
| − | * [https://hub.docker.com/r/statisticalgenetics/plink-gwas PLINK GWAS | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Questions.pdf PLINK GWAS: Data QC Questions [PDF]] |
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Answers.pdf PLINK GWAS: Data QC Answers [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure.pdf PLINK GWAS: Population Substructure Exercise [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure_Outputs.pdf PLINK GWAS: Population Substructure Output [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure_Questions.pdf PLINK GWAS: Population Substructure Questions [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure_Answers.pdf PLINK GWAS: Population Substructure Answers [PDF]] | ||
| + | * [https://hub.docker.com/r/statisticalgenetics/plink-gwas PLINK GWAS Docker Image] | ||
To pull and download the docker image from the Docker Hub repository, | To pull and download the docker image from the Docker Hub repository, | ||
| Line 64: | Line 79: | ||
<pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas</pre> | <pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas</pre> | ||
| + | |||
| + | ==Power Analysis== | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Power_Calculations_Questions.pdf Power Analysis Questions [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Power_Calculations_Answers.pdf Power Analysis Answers [PDF]] | ||
==REGENIE== | ==REGENIE== | ||
| − | * [ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie.pdf Regenie Exercise [PDF]] |
| − | * [https://hub.docker.com/r/statisticalgenetics/regenie | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie_Outputs.pdf Regenie Output [PDF]] |
| + | * [https://hub.docker.com/r/statisticalgenetics/regenie Regenie Docker Image] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie_Questions.pdf Regenie Questions [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie_Answers.pdf Regenie 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, | ||
| Line 76: | Line 98: | ||
<pre>docker run --rm -p 8888:8888 statisticalgenetics/regenie</pre> | <pre>docker run --rm -p 8888:8888 statisticalgenetics/regenie</pre> | ||
| − | ==Regression and Intro to | + | ==Regression and Intro to PLINK and R== |
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/Regression.pdf Regression Exercise [PDF]] |
| − | * [[ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Outputs.pdf Regression Output [PDF]] |
| − | * [https://hub.docker.com/r/statisticalgenetics/regression-plink-r Regression and Intro to PLINK & R | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Questions.pdf Regression Questions [PDF]] |
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Answers.pdf Regression Answers [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Intro_Plink_R.pdf Intro to PLINK & R Exercise [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Intro_Plink_R_Outputs.pdf Intro to PLINK & R Output [PDF]] | ||
| + | * [https://hub.docker.com/r/statisticalgenetics/regression-plink-r Regression and Intro to PLINK & R Docker Image] | ||
To pull and download the docker image from the Docker Hub repository, | To pull and download the docker image from the Docker Hub repository, | ||
| Line 89: | Line 115: | ||
<pre>docker run --rm -p 8888:8888 statisticalgenetics/regression-plink-r</pre> | <pre>docker run --rm -p 8888:8888 statisticalgenetics/regression-plink-r</pre> | ||
| + | |||
| + | ==Pencil and Paper Exercise== | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Population_Genetics_Questions.pdf Population Genetics Questions [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Population_Genetics_Answers.pdf Population Genetics Answers [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Linkage_Disequilibrium_Questions.pdf Linkage Disequilibrium Questions [PDF]] | ||
| + | * [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Linkage_Disequilibrium_Answers.pdf Linkage Disequilibrium Answers [PDF]] | ||
Latest revision as of 14:58, 10 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
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 [PDF]
- PLINK GWAS: Data QC Output [PDF]
- PLINK GWAS: Data QC Questions [PDF]
- PLINK GWAS: Data QC Answers [PDF]
- PLINK GWAS: Population Substructure Exercise [PDF]
- PLINK GWAS: Population Substructure Output [PDF]
- PLINK GWAS: Population Substructure Questions [PDF]
- PLINK GWAS: Population Substructure Answers [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
Power Analysis
REGENIE
- Regenie Exercise [PDF]
- Regenie Output [PDF]
- Regenie Docker Image
- Regenie Questions [PDF]
- Regenie Answers [PDF]
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]
- Regression Output [PDF]
- Regression Questions [PDF]
- Regression Answers [PDF]
- Intro to PLINK & R Exercise [PDF]
- Intro to PLINK & R Output [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
