Difference between revisions of "Tutorials"
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==Tutorials for Courses== | ==Tutorials for Courses== | ||
* [[Tutorials#FastLMM_&_GCTA|FastLMM & GCTA]] | [[Media:fastlmm_gcta_exercise.pdf|exercise [PDF]]] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta docker image] | * [[Tutorials#FastLMM_&_GCTA|FastLMM & GCTA]] | [[Media:fastlmm_gcta_exercise.pdf|exercise [PDF]]] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta docker image] | ||
| − | * Mendelian Randomization | exercise [PDF] and docker image | + | * [[Tutorials#Mendelian Randomization|Mendelian Randomization]] | exercise [PDF] and docker image |
* [[Tutorials#Pleiotropy|Pleiotropy]] | exercise [PDF] and docker image | * [[Tutorials#Pleiotropy|Pleiotropy]] | exercise [PDF] and docker image | ||
| − | * PLINK GWAS: QC and Controlling for Population | + | * [[Tutorials#PLINK_GWAS:_Data_Quality_Control_and Association_Analysis_Controlling_for_Population_Substructure|PLINK GWAS: QC and Controlling for Population Substructure]] | [[Media:PLINK_Data_QC.pdf|QC exercise [PDF]]], [[Media:PLINK_Substructure.pdf|Substructure exercise [PDF]]], and [https://hub.docker.com/r/statisticalgenetics/plink-gwas docker image] |
| − | * | + | * [[Tutorials#REGENIE|REGENIE]] | [[Media:regenie.pdf|exercise [PDF]]] and [https://hub.docker.com/r/statisticalgenetics/regenie docker image] |
| − | * | + | * [[Tutorials#Regression_and_Intro_to_PLINK_and_R|Regression and Intro to PLINK and R]] | [[Media:Regression.pdf|Regression exercise [PDF]]], [[Media:Intro_Plink_R.pdf|Intro to PLINK & R exercise[PDF]]], and [https://hub.docker.com/r/statisticalgenetics/regression-plink-r docker image] |
==Running Tutorials on Your Computer== | ==Running Tutorials on Your Computer== | ||
| Line 11: | Line 11: | ||
===General instructions=== | ===General instructions=== | ||
| − | * [[Media:Statistical_Genetics_Exercise_Instructions.pdf| | + | * [[Media: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 38: | Line 38: | ||
To run the exercise from the downloaded docker image, | To run the exercise from the downloaded docker image, | ||
| − | <pre>docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization | + | <pre>docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization</pre> |
| + | |||
==Pleiotropy== | ==Pleiotropy== | ||
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.pdf Pleiotropy Exercise <nowiki>[PDF]</nowiki>] | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.pdf Pleiotropy Exercise <nowiki>[PDF]</nowiki>] | ||
| Line 49: | Line 50: | ||
<pre>docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy</pre> | <pre>docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy</pre> | ||
| − | + | ||
| − | ==PLINK GWAS: Data Quality Control | + | ==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. | These exercises run using a shared docker image, however the exercises are split into two separate notebooks. | ||
| − | * PLINK GWAS: Data | + | * [[Media:PLINK_Data_QC.pdf|PLINK GWAS: Data QC Exercise <nowiki>[PDF]</nowiki>]] |
| − | * PLINK GWAS: Population | + | * [[Media:PLINK_Substructure.pdf|PLINK GWAS: Population Substructure Exercise <nowiki>[PDF]</nowiki>]] |
| − | * PLINK GWAS docker image | + | * [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 62: | Line 63: | ||
To run the exercise from the downloaded docker image, | To run the exercise from the downloaded docker image, | ||
| − | <pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas | + | <pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas</pre> |
| + | |||
==REGENIE== | ==REGENIE== | ||
| − | * | + | * [[Media:regenie.pdf|Regenie Exercise <nowiki>[PDF]</nowiki>]] |
| − | * [https:// | + | * [https://hub.docker.com/r/statisticalgenetics/regenie Regenie 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 73: | Line 75: | ||
<pre>docker run --rm -p 8888:8888 statisticalgenetics/regenie</pre> | <pre>docker run --rm -p 8888:8888 statisticalgenetics/regenie</pre> | ||
| − | |||
==Regression and Intro to PLINK and R== | ==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. | ||
| − | * | + | * [[Media:Regression.pdf|Regression exercise [PDF]]] |
| − | * | + | * [[Media:Intro_Plink_R.pdf|Intro to PLINK & R Exercise <nowiki>[PDF]</nowiki>]] |
| − | + | * [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, | ||
Latest revision as of 20:33, 17 August 2026
Contents
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
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 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
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
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
