Difference between revisions of "Tutorials"
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* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#alternative-to-cloud-server-use-your-own-computer Instructions to setup course tutorial environment on your computer] | * [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#alternative-to-cloud-server-use-your-own-computer Instructions to setup course tutorial environment on your computer] | ||
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-1-launch-exercise-in-jupyterlab Instructions to run course tutorial through JupyterLab] | * [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-1-launch-exercise-in-jupyterlab Instructions to run course tutorial through JupyterLab] | ||
| − | * [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials# | + | * [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-2-launch-from-command-shell Instructions to run course tutorial through command line terminal] |
Revision as of 20:43, 1 November 2021
Contents
- 1 Running Tutorials on Your Computer
- 2 Alohomora
- 3 Annotation
- 4 Annovar MEndelian
- 5 Cochran Armitage Trend Test
- 6 Epistasis (PLINK and CASSI)
- 7 FastLMM
- 8 GCTA
- 9 Gemini
- 10 Genehunter
- 11 GWAS: Data Quality Control
- 12 GWAS: Association Analysis Controlling for Population Substructure
- 13 Homozygosity Mapper
- 14 IGV
- 15 Linkage/FastLinkage
- 16 Pleiotropy
- 17 Polygenic risk prediction (NPS method)
- 18 Population Genetics
- 19 PSEQ
- 20 Regression
- 21 RV-TDT
- 22 SEQLinkage
- 23 SEQSpark
- 24 SLINK
- 25 SUPERLINK
- 26 Variant Association Tools
Running Tutorials on Your Computer
Starting Fall 2019 we adopt docker to run our course material . We have created various docker repositories with source material freely available from github for users to readily setup and reproduce our tutorials on their own computers. These docker images can also be used as production tool to run relevant software on your computer (Mac, Linux or Windows) or even a high performance computing cluster (if properly configured) for your own data analysis.
- Instructions to setup course tutorial environment on your computer
- Instructions to run course tutorial through JupyterLab
- Instructions to run course tutorial through command line terminal
Tutorial specific instructions
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.
Alohomora
Annotation
To run the exercise from docker image provided,
statgen-setup login --tutorial annovar
The "statgen-setup" script is available here and can be installed following these instructions.
Annovar MEndelian
Cochran Armitage Trend Test
Epistasis (PLINK and CASSI)
To run the exercise from docker image provided,
statgen-setup login --tutorial epistasis
The "statgen-setup" script is available here and can be installed following these instructions.
FastLMM
To run the exercise from docker image provided,
statgen-setup login --tutorial fastlmm-gcta
The "statgen-setup" script is available here and can be installed following these instructions.
GCTA
To run the exercise from docker image provided,
statgen-setup login --tutorial fastlmm-gcta
The "statgen-setup" script is available here and can be installed following these instructions.
Gemini
To run the exercise from docker image provided,
statgen-setup login --tutorial gemini
The "statgen-setup" script is available here and can be installed following these instructions.
Genehunter
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install genehunter-tutorial
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
To run the exercise from docker image provided,
statgen-setup login --tutorial plink
The "statgen-setup" script is available here and can be installed following these instructions.
GWAS: Association Analysis Controlling for Population Substructure
To run the exercise from docker image provided,
statgen-setup login --tutorial plink
The "statgen-setup" script is available here and can be installed following these instructions.
Homozygosity Mapper
IGV
To run the exercise from docker image provided,
statgen-setup login --tutorial igv
The "statgen-setup" script is available here and can be installed following these instructions.
Linkage/FastLinkage
To run the exercise from docker image provided,
statgen-setup login --tutorial mlink
The "statgen-setup" script is available here and can be installed following these instructions.
Pleiotropy
To run the exercise from docker image provided,
statgen-setup login --tutorial pleiotropy
The "statgen-setup" script is available here and can be installed following these instructions.
Polygenic risk prediction (NPS method)
To run the exercise from docker image provided,
statgen-setup login --tutorial nps
The "statgen-setup" script is available here and can be installed following these instructions.
Population Genetics
To run the exercise from docker image provided,
statgen-setup login --tutorial popgen
The "statgen-setup" script is available here and can be installed following these instructions.
PSEQ
To run the exercise from docker image provided,
statgen-setup login --tutorial pseq
The "statgen-setup" script is available here and can be installed following these instructions.
Regression
To run the exercise from docker image provided,
statgen-setup login --tutorial regression
The "statgen-setup" script is available here and can be installed following these instructions.
RV-TDT
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install rvtdt-tutorial
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
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install seqlinkage-tutorial
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
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install seqspark-tutorial
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
To run the exercise from docker image provided,
statgen-setup login --tutorial slink
The "statgen-setup" script is available here and can be installed following these instructions.
SUPERLINK
Variant Association Tools
To run the exercise from docker image provided,
statgen-setup login --tutorial vat
The "statgen-setup" script is available here and can be installed following these instructions.
