Difference between revisions of "Tutorials"

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===General instructions===
 
===General instructions===
 
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#alternative-to-cloud-server-use-your-own-computer Instructions to install Docker Desktop and running the course material on your computer]<br /><br />
 
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#alternative-to-cloud-server-use-your-own-computer Instructions to install Docker Desktop and running the course material on your computer]<br /><br />
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−
===Preparing Your Computer===
 
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{| class="wikitable"
 
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|-
 
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||{{#ev:youtube|3K-sGzxsyK0|240|center|Linux}}
 
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||{{#ev:youtube|DRCDNBlxZ-w|240|center|Mac}}
 
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||{{#ev:youtube|sxv45NCSFMk|240|center|Windows}}
 
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|}
 
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===Running Exercises===
 
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{{#ev:youtube|OgHvRVtIIog|320}}
 
  
 
===Tutorial specific instructions===
 
===Tutorial specific instructions===
−
We use a script [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup "statgen-setup"] to start the docker based environments for these tutorials. Please refer to the previous section for instructions on the installation of this script.
+
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 (''only those using statgen-setup command are relevant to our docker based tutorials''). They provide links to materials and a minimal set of commands to use for launching and running an exercise. Command "statgen-setup login" will allow you to start and login to a Linux command line environment (regardless of your current computational environment) to perform all analysis in command shells. This works for all the tutorials on this page. Additionally, some tutorials support command "statgen-setup launch" which will start a JupyterLab server to perform the analysis.
+
−
 
+
  
 +
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==
−
* [[Media:fastlmm_gcta_exercise.pdf|FastLMM & GCTA exercise]]
+
* [[Media:fastlmm_gcta_exercise.pdf|FastLMM & GCTA exercise]] [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf <nowiki>[PDF]</nowiki>]
 
* [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta FastLMM & GCTA docker image]
 
* [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta FastLMM & GCTA docker image]
  
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/fastlmm-gcta</pre>
 
<pre>docker run --rm -p 8888:8888 statisticalgenetics/fastlmm-gcta</pre>
  
−
==Fine-mapping (SuSiE method)==
+
==Mendelian Randomization==
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping.docx susieR Exercise <nowiki>[DOCX]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf Mendelian Randomization exercise <nowiki>[PDF]</nowiki>]
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping_answers.docx susieR Exercise Answers <nowiki>[DOCX]</nowiki>]
+
* Mendelian Randomization docker image
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping.ipynb susieR Exercise <nowiki>[Ipython notebook]</nowiki>]
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping_answers.ipynb susieR Exercise Answers <nowiki>[Ipython notebook]</nowiki>]
+
  
 +
To pull and download the docker image from the Docker Hub repository,
  
−
To run the exercise from docker image provided,
+
<pre>docker pull statisticalgenetics/mendelian-randomization</pre>
−
 
+
To run the exercise from the downloaded docker image,
−
<pre>statgen-setup launch --tutorial finemap
+
−
</pre>
+
−
 
+
−
==GCTA==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf GCTA exercise <nowiki>[PDF]</nowiki>]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial fastlmm-gcta
+
−
</pre>
+
−
 
+
−
 
+
−
==Gemini==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[DOCX]</nowiki>]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial gemini
+
−
</pre>
+
−
 
+
−
 
+
−
==Genehunter==
+
−
* [http://statgen.us/files/tutorials/genehunter/Mult_Genehunter.pdf <nowiki>[PDF]</nowiki>]
+
−
* [[Genehunter Exercise|Exercise Commands]]
+
−
 
+
−
 
+
−
To install from packages, follow the configuration steps above and run the following command.
+
−
 
+
−
<pre>sudo apt-get install genehunter-tutorial</pre>
+
−
The exercise's files will then be installed in the folder ''/home/shared/genehunter''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
+
−
 
+
−
==GWAS: Data Quality Control==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Data_QC.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
+
−
* [[GWAS Data QC Exercise|Exercise Commands]]
+
−
 
+
−
To run the exercise via JupyterLab from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial plink
+
−
</pre>
+
−
 
+
−
Alternatively, you can opt to run the exercise via command terminal from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial plink
+
−
</pre>
+
−
 
+
−
==GWAS: Association Analysis Controlling for Population Substructure==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_Substructure.pdf Exercise <nowiki>[PDF]</nowiki>]
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−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Substructure.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
+
−
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
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−
 
+
−
To run the exercise via JupyterLab from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial plink
+
−
</pre>
+
−
 
+
−
Alternatively, you can opt to run the exercise via command terminal from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial plink
+
−
</pre>
+
−
 
+
−
==Homozygosity Mapper==
+
−
* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]
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−
* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]
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* [http://www.homozygositymapper.org Data Sets]
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−
 
+
−
==IGV==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/IGV.docx IGV exercise <nowiki>[DOCX]</nowiki>]
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−
* [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)]
+
−
 
+
−
 
+
−
 
+
−
==Linkage/FastLinkage==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/MLINK.pdf LINKAGE Exercise <nowiki>[DOCX]</nowiki>]
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial mlink
+
−
</pre>
+
−
 
+
−
==LD clumping==
+
−
* [https://github.com/cumc/bioworkflows/blob/master/GWAS/LD_Clumping.ipynb LD Clumping Exercise <nowiki>[IPython Notebook]</nowiki>]
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial clumping
+
−
</pre>
+
−
 
+
−
==MR-JTI for TWAS==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/MR_JTI.ipynb MR-JTI Exercise <nowiki>[IPython Notebook]</nowiki>]
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial twas
+
−
</pre>
+
  
 +
<pre>docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization<br /><br /></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>]
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Answers to Questions <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy docker image]
  
−
To run the exercise from docker image provided,
+
To pull and download the docker image from the Docker Hub repository,
  
−
<pre>statgen-setup login --tutorial pleiotropy
+
<pre>docker pull statisticalgenetics/pleiotropy</pre>
−
</pre>
+
To run the exercise from the downloaded docker image,
  
 +
<pre>docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy</pre>
 +
<pre> </pre>
 +
==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.
  
−
==Polygenic risk prediction (NPS method)==
+
* PLINK GWAS: Data QC [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/NPS.pdf PRS NPS Exercise <nowiki>[DOCX]</nowiki>]
+
* PLINK GWAS: Population Substructure [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
 +
* PLINK GWAS docker image
  
−
To run the exercise from docker image provided,
+
To pull and download the docker image from the Docker Hub repository,
−
 
+
−
<pre>statgen-setup login --tutorial nps
+
−
</pre>
+
−
 
+
−
 
+
−
==Polygenic risk prediction (LDpred2 method)==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/ldpred2_example.pdf PRS LDpred2 Exercise <nowiki>[PDF]</nowiki>]
+
−
* [https://github.com/cumc/bioworkflows/blob/master/ldpred/ldpred2_example.ipynb PRS LDpred2 Exercise <nowiki>[Ipython Notebook]</nowiki>]
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial ldpred2
+
−
</pre>
+
−
 
+
−
Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type
+
−
 
+
−
<pre>get-data</pre>
+
−
 
+
−
to load the data-set to the JupyterLab workspace.
+
−
 
+
−
 
+
−
<!--
+
−
==Population Genetics==
+
−
* [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_exercise.pdf Population Exercise <nowiki>[PDF]</nowiki>]
+
−
* [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_answers.pdf Exercise Answers <nowiki>[PDF]</nowiki>]
+
−
* [http://statgen.us/files/tutorials/population/popgen_drift.q Commands for popgen_drift]
+
−
* [http://statgen.us/files/tutorials/population/popgen_selection.q Commands for popgen_selection]
+
−
-->
+
−
==Population Genetics==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PopGen.docx Popgen Exercise <nowiki>[DOCX]</nowiki>]
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial popgen
+
−
</pre>
+
−
 
+
−
 
+
−
==PSEQ==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PSEQ.ipynb PSEQ Exercise <nowiki>[Ipython Notebook]</nowiki>]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial pseq
+
−
</pre>
+
−
 
+
−
Notice that since PSEQ exercise does not involve generating and visualizing plots, it is also fine to use a command terminal, instead of the JupyterLab server, to run this exercise and reproduce exactly what was described in the tutorial. To do so,
+
−
 
+
−
<pre>statgen-setup login --tutorial pseq
+
−
</pre>
+
−
 
+
−
 
+
−
==R and PLINK==
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial plink-r-nothnagel
+
−
</pre>
+
  
 +
<pre>docker pull statisticalgenetics/plink-gwas</pre>
 +
To run the exercise from the downloaded docker image,
  
 +
<pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas<br /><br /></pre>
 
==REGENIE==
 
==REGENIE==
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regenie_example.pdf REGENIE Exercise <nowiki>[PDF]</nowiki>]
+
* Regenie [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.pdf Exercise <nowiki>[PDF]</nowiki>]
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/regenie_example.ipynb REGENIE Exercise <nowiki>[Ipython Notebook]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Regenie docker image]
  
 +
To pull and download the docker image from the Docker Hub repository,
  
−
To run the exercise from docker image provided,
+
<pre>docker pull statisticalgenetics/regenie</pre>
 +
To run the exercise from the downloaded docker image,
  
−
<pre>statgen-setup launch --tutorial regenie
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/regenie</pre>
−
</pre>
+
  
−
Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type
 
  
−
<pre>get-data</pre>
+
==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 load the data-set to the JupyterLab workspace.
+
* Regression [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
 +
* Intro to PLINK and R [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
 +
* Regression and Intro to PLINK & R docker image
  
 +
To pull and download the docker image from the Docker Hub repository,
  
 +
<pre>docker pull statisticalgenetics/regression-plink-r</pre>
 +
To run the exercise from the downloaded docker image,
  
−
==Regression==
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/regression-plink-r</pre>
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regression.docx Regression Exercise <nowiki>[DOCX]</nowiki>]
+
−
* [[Regression_Exercise|Exercise Commands]]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial regression
+
−
</pre>
+
−
 
+
−
 
+
−
==RV-TDT==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/RV-TDT.doc Exercise <nowiki>[DOC]</nowiki>]
+
−
* [[RV-TDT|Exercise Commands]]
+
−
 
+
−
====Installing Packages====
+
−
To install from packages, follow the configuration steps above and run the following command.
+
−
 
+
−
<pre>sudo apt-get install rvtdt-tutorial</pre>
+
−
The exercise's files will then be installed in the folder ''/home/shared/rvtdt''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
+
−
 
+
−
==SEQLinkage==
+
−
* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[SEQLinkage_Commands_in_Exercise|Exercise Commands]]
+
−
 
+
−
 
+
−
To install from packages, follow the configuration steps above and run the following command.
+
−
 
+
−
<pre>sudo apt-get install seqlinkage-tutorial</pre>
+
−
The exercise's files will then be installed in the folder ''/home/shared/seqlinkage''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
+
−
 
+
−
==SEQSpark==
+
−
* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[SEQSpark|Exercise Commands]]
+
−
* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
+
−
 
+
−
====Installing Packages====
+
−
To install from packages, follow the configuration steps above and run the following command.
+
−
 
+
−
<pre>sudo apt-get install seqspark-tutorial</pre>
+
−
The exercise's files will then be installed in the folder ''/home/shared/seqspark''. You can run from there or copy the files into your user's home directory and proceed with the exercise.In order for the
+
−
commands to work correctly, you don't need to reboot, but you should log out and log back in to make sure that the computer's environment is correctly configured.
+
−
 
+
−
==SLINK==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Slink.doc SLINK Exercise <nowiki>[DOCX]</nowiki>]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial slink</pre>
+
−
 
+
−
==SUPERLINK==
+
−
* [http://statgen.us/files/tutorials/Superlink_Exercise_v2.pdf SUPERLINK Exercise <nowiki>[PDF]</nowiki>]
+
−
* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]
+
−
 
+
−
==Variant Association Tools==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/VAT.docx VAT Exercise <nowiki>[DOCX]</nowiki>]
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Exercise <nowiki>[Ipython notebook]</nowiki>]
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial vat
+
−
</pre>
+
−
 
+
−
Then follow the prompts on the terminal output to open up the JupyterLab server in your web browser. You should find the exercise notebook in the side panel, and you can click to open it.
+

Revision as of 19:02, 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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