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__NOTOC__
 
__NOTOC__
  
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==Welcome to the Center for Statistical Genetics==
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==Statistical Genetics Training Resources==
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We are a group of statistical geneticists in [http://columbianeuroresearch.org/sergievsky/ The Gertrude H. Sergievsky Center] and [http://www.columbianeurology.org/ Department of Neurology] at [https://www.ps.columbia.edu Columbia University Vagelos College of Physicians and Surgeons] in New York City. We focus on both the research and education of statistical genetics and genetic epidemiology.
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We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.
  
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On this website you will find research profiles of our faculty, trainees and visiting scholars, courses we teach and software we develop.
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===Our group===
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* Heather Cordell, Ph.D. (Newcastle University)
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* Andrew DeWan, Ph.D. (Yale University)
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* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
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* Michael Nothnagel, Ph.D. (University of Cologne)
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* Gao T. Wang, Ph.D. (Columbia University)
  
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: [[news|<span style="font-size: large; color: #800000;"> ☛ Read Our News </span>]]
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Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses
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==Faculty==
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* [[Suzanne_M_Leal_PhD|Suzanne M. Leal, Ph.D.]], Professor and Director
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* [http://www.columbianeurology.org/profile/ischrauwen?profile=researcher Isabelle Schrauwen, Ph.D.], Assistant Professor
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* [https://www.tigerwang.org/ Gao Wang, Ph.D.], Assistant Professor
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==Trainees and staff members==
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For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions
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===Current members===
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* Anushree Acharya, Research Assistant
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* Thashi Bharadwaj, Postdoc Researcher
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* Diana Cornejo, Postdoc Researcher
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* [[Nadia_Farooqi | Nadia Farooqi]], Visiting PhD Student
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* Liz M Nouel, Research Assistant
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* Zhiying Xie, Visiting PhD Student
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===Alumni===
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Please find [[alumni|on this page]] previous personnel, visiting scholars and rotation students.
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==Statistical Genetics Courses==
 
==Statistical Genetics Courses==
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[[Advgenemap2020|Advanced Gene Mapping Course]]<br />January 27-31, 2020<br />The Rockefeller University, New York, USA
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'''[[Genassoc2024|Genetic Association: with application to sequence and genotype data]]'''<br />September 16-20, 2024<br />Max Delbrück Center for Molecular Medicine, Berlin, Germany
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<br /><br />
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[[ComplexNGS2019|Complex Trait Analysis of Next Generation Sequence Data]]<br />November 11-15, 2019<br />Max Delbrück Center for Molecular Medicine, Berlin, Germany
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'''[[Advgenemap2025|Advanced Gene Mapping]]'''<br />January 27-31, 2025<br />The Rockefeller University, New York, USA
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<br /><br />
 
[[Previous_Courses|Previous Course Pages]]
 
[[Previous_Courses|Previous Course Pages]]
  
 
==Tutorials for Courses==
 
==Tutorials for Courses==
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* [[Tutorials#Annotation|Annotation]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/annovar.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/annovar/tags docker image]
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* [[Tutorials#Annotation|ANNOVAR Annotation]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/annovar.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/annovar/tags docker image]
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* [[Tutorials#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test]]
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* [[Tutorials#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
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* [[Tutorials#GATK|GATK and IGV]]
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* [[Tutorials#FastLMM | Family-based Association using FaST-LMM, PLINK and R]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image]
 
* [[Tutorials#IGV|IGV]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/igv.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/igv/tags docker image]
 
* [[Tutorials#IGV|IGV]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/igv.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/igv/tags docker image]
 
* [[Tutorials#Gemini|Gemini]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/gemini.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/gemini/tags docker image]
 
* [[Tutorials#Gemini|Gemini]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/gemini.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/gemini/tags docker image]
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* [[Tutorials#GenABEL|GenABEL]]
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* [[Tutorials#GCTA|GCTA]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image]
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* [[Tutorials#GWAS:_Data_Quality_Control|GWAS: QC]]
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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/plink/tags docker image]
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* [[Tutorials#GWAS:_Association_Analysis_Controlling_for_Population_Substructure|GWAS: Controlling for Population Substructure]]
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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#SLINK|LINKAGE]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/mlink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/mlink/tags docker image]
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* [[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]
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* [[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]
 
* [[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]
 
* [[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]
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* [[Tutorials#PSEQ|PSEQ]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pseq.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/pseq/tags docker image]
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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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* [[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]
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* [[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]
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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]
 
* [[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]
 
* [[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]
 
* [[Tutorials#RV-TDT|RV-TDT]]
 
* [[Tutorials#RV-TDT|RV-TDT]]
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* [[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]
 
* [[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]
  
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<!--
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<!---
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===SeqSpark===
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* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf PDF]
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* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
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* [[Tutorials#SEQSpark|Instructions for package installation]]
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-->
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==Statistical Genetics Software==
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* [https://github.com/gaow/kbac KBAC]
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* [https://github.com/statgenetics/mendelprob MendelProb]
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* [https://code.google.com/p/phenoman/ PhenoMan] | [https://github.com/statgenetics/phenoman now on github]
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* [http://bioinformatics.org/simped/rare/ RarePedSim] | [https://github.com/statgenetics/rarepedsim now on github]
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* [http://www.bioinformatics.org/rv-gdt/ RV-GDT] | [https://github.com/statgenetics/rv-gdt now on github]
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* [http://bioinformatics.org/rv-tdt/wiki/ RV-TDT] | [https://github.com/statgenetics/rv-gdt now on github]
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* [https://github.com/statgenetics/rvnpl RV-NPL]
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* [http://www.bioinformatics.org/seqlink/ SEQLinkage] | [https://github.com/gaow/SEQLinkage source on github]
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* [http://www.bioinformatics.org/spower/start SEQPower] | [https://github.com/gaow/SEQPower source on github]
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* [https://github.com/statgenetics/seqspark SEQSpark]
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* [http://bioinformatics.org/simped SimPed] | [https://github.com/statgenetics/simped now on github]
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* [https://code.google.com/p/simrare/ SimRare] | [https://github.com/statgenetics/simrare now on github]
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* [http://varianttools.sourceforge.net/Association/HomePage Variant Association Tools] | [https://github.com/vatlab/varianttools now on github]
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* [[VMT|Variant Mendelian Tools]]
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==[[Genetic Meetings of Interest]]==
 
==[[Genetic Meetings of Interest]]==
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<!---
 
 
[[NGSMendelian2017|Identifying Genes for Mendelian Traits using Next Generation Sequence Data]], September 18-22, 2017<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
 
[[NGSMendelian2017|Identifying Genes for Mendelian Traits using Next Generation Sequence Data]], September 18-22, 2017<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
  

Latest revision as of 05:40, 19 June 2024


Statistical Genetics Training Resources

We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

Our group

  • Heather Cordell, Ph.D. (Newcastle University)
  • Andrew DeWan, Ph.D. (Yale University)
  • Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
  • Michael Nothnagel, Ph.D. (University of Cologne)
  • Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

Statistical Genetics Courses

Genetic Association: with application to sequence and genotype data
September 16-20, 2024
Max Delbrück Center for Molecular Medicine, Berlin, Germany

Advanced Gene Mapping
January 27-31, 2025
The Rockefeller University, New York, USA

Previous Course Pages

Tutorials for Courses


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