Difference between revisions of "Tutorials"

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==Tutorials for Courses==
 
==Tutorials for Courses==
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* [[Tutorials#FastLMM_&_GCTA|FastLMM & GCTA]] | [[Media:fastlmm_gcta_exercise.pdf|exercise[PDF]]] [PDF and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta docker image]
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* [[Tutorials#FastLMM_&_GCTA|FastLMM & GCTA]] | [[Media:fastlmm_gcta_exercise.pdf|exercise [PDF]]] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta docker image]
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* [[Tutorials#GWAS:_Data_Quality_Control|GWAS: QC]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/plink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta docker image]
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* Mendelian Randomization | exercise [PDF] and docker image
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* [[Tutorials#GWAS:_Association_Analysis_Controlling_for_Population_Substructure|GWAS: Controlling for Population Substructure]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/plink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/plink/tags docker image]
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* [[Tutorials#Pleiotropy|Pleiotropy]] | exercise [PDF] and docker image
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* Mendelian Randomization | docker image and exercise
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* 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]
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* <s>[[Tutorials#Epistasis_.28PLINK_and_CASSI.29 | Interaction analysis using PLINK and CASSI]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/epistasis.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/epistasis/tags docker image]</s>
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* Regression and Intro to PLINK & 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]
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* <s>[[Tutorials#Linkage.2FFastLinkage|LINKAGE]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/mlink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/mlink/tags docker image]</s>
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* REGENIE | [[Media:regenie.pdf|exercise [PDF]]] and [https://hub.docker.com/r/statisticalgenetics/regenie docker image]<s></s>
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* <s>[[Tutorials#Population_Genetics|Population Genetics]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/popgen.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/popgen/tags docker image]</s>
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* [[Tutorials#Pleiotropy|Pleiotropy]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pleiotropy.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/pleiotropy/tags docker image]
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* <s>[[Tutorials#Polygenic_risk_prediction_.28NPS_method.29|Polygenic risk prediction using non-parametric shrinkage]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/nps.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/nps/tags docker image]</s>
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* <s>[[Tutorials#PSEQ|PLINK/SEQ (PSEQ)]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pseq.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/pseq/tags docker image]</s>
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* [[Tutorials#R_and_PLINK|R and PLINK exercise]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/plink-r-nothnagel.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/plink-r-nothnagel/tags docker image]
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* [[Tutorials#Regression|Regression]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/regression.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/regression/tags docker image]
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* <s>[[Tutorials#RV-TDT|RV-TDT]]</s>
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* <s>[[Tutorials#SEQLinkage|SEQLinkage]]</s>
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* <s>[[Tutorials#SEQSpark|SEQSpark]]</s>
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* <s>[[Tutorials#SLINK|SLINK]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/slink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/slink/tags docker image]</s>
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* <s>[[Tutorials#Variant_Association_Tools|Variant Association Tools]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/vat.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/vat/tags docker image]</s>
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==Running Tutorials on Your Computer==
 
==Running Tutorials on Your Computer==

Revision as of 20:04, 17 August 2026

Tutorials for Courses

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

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<br /><br />

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.

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<br /><br />

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.

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
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