Difference between revisions of "Main Page"

From Statistical Genetics Courses

Jump to: navigation, search
(Tutorials for Courses)
(Statistical Genetics Courses)
 
(75 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
  
==Welcome to the Center for Statistical Genetics==
+
==Statistical Genetics Training Resources==
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.
+
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.
  
On this website you will find research profiles of our faculty, trainees and visiting scholars, courses we teach and software we develop.
+
===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)
  
: [[news|<span style="font-size: large; color: #800000;"> ☛ Read Our News </span>]]
+
Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses
==Faculty==
+
* [[Suzanne_M_Leal_PhD|Suzanne M. Leal, Ph.D.]], Professor and Director
+
* [http://www.columbianeurology.org/profile/ischrauwen?profile=researcher Isabelle Schrauwen, Ph.D.], Assistant Professor
+
* [https://www.tigerwang.org/ Gao Wang, Ph.D.], Assistant Professor
+
  
==Trainees and staff members==
+
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
===Current members===
+
* Anushree Acharya, Research Assistant
+
* Thashi Bharadwaj, Postdoc Researcher
+
* Diana Cornejo, Postdoc Researcher
+
* [[Nadia_Farooqi | Nadia Farooqi]], Visiting PhD Student
+
* Liz M Nouel, Research Assistant
+
* [[Zhiying_Xie | Zhiying Xie]], Visiting PhD Student
+
 
+
===Alumni===
+
Please find [[alumni|on this page]] previous personnel, visiting scholars and rotation students.
+
  
 
==Statistical Genetics Courses==
 
==Statistical Genetics Courses==
<!--[[Genassoc2020|Genetic Association]]-->Genetic Association<br />June 22-26, 2020<br />Max Delbrück Center for Molecular Medicine, Berlin, Germany
+
'''[[Genassoc2024|Genetic Association: with application to sequence and genotype data]]'''<br />September 16-20, 2024<br />Max Delbrück Center for Molecular Medicine, Berlin, Germany
 
+
<br /><br />
<!--[[ComplexNGS2020|Complex Trait Analysis of Next Generation Sequence Data]]-->Complex Trait Analysis of Next Generation Sequence Data<br />November 23-27, 2020<br />Max Delbrück Center for Molecular Medicine, Berlin, Germany
+
'''[[Advgenemap2025|Advanced Gene Mapping]]'''<br />January 27-31, 2025<br />The Rockefeller University, New York, USA
 
+
<br /><br />
<!--[[Advgenemap2021|Advanced Gene Mapping]]-->Advanced Gene Mapping<br /> January 25-29, 2021 (Tentative Dates)<br />The Rockefeller University, New York, USA
+
 
+
 
[[Previous_Courses|Previous Course Pages]]
 
[[Previous_Courses|Previous Course Pages]]
  
 
==Tutorials for Courses==
 
==Tutorials for Courses==
* [[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]
+
* [[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]
 
* [[Tutorials#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
 
* [[Tutorials#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[Tutorials#family_gwas | 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#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]
Line 42: Line 31:
 
* [[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]
 
* [[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]
 
* [[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]
 
* [[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]
* [[Tutorials#Epistasis_PLINK_CASSI | 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]
+
* [[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]
* [[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]
+
* [[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]
* [[Tutorials#pleitrophy|Pleitropy]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pleiotropy.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/pleiotropy/tags docker image]
+
* [[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]
* [[Tutorials#NPS|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]
+
* [[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]
* [[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]
+
* [[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]
 +
* [[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]]
Line 55: Line 45:
 
* [[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]
  
<!--
+
<!---
===SeqSpark===
+
* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf PDF]
+
* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
+
* [[Tutorials#SEQSpark|Instructions for package installation]]
+
-->
+
 
+
==Statistical Genetics Software==
+
* [https://github.com/gaow/kbac KBAC]
+
* [https://github.com/statgenetics/mendelprob MendelProb]
+
* [https://code.google.com/p/phenoman/ PhenoMan] | [https://github.com/statgenetics/phenoman now on github]
+
* [http://bioinformatics.org/simped/rare/ RarePedSim] | [https://github.com/statgenetics/rarepedsim now on github]
+
* [http://www.bioinformatics.org/rv-gdt/ RV-GDT] | [https://github.com/statgenetics/rv-gdt now on github]
+
* [http://bioinformatics.org/rv-tdt/wiki/ RV-TDT] | [https://github.com/statgenetics/rv-gdt now on github]
+
* [https://github.com/statgenetics/rvnpl RV-NPL]
+
* [http://www.bioinformatics.org/seqlink/ SEQLinkage] | [https://github.com/gaow/SEQLinkage source on github]
+
* [http://www.bioinformatics.org/spower/start SEQPower] | [https://github.com/gaow/SEQPower source on github]
+
* [https://github.com/statgenetics/seqspark SEQSpark]
+
* [http://bioinformatics.org/simped SimPed] | [https://github.com/statgenetics/simped now on github]
+
* [https://code.google.com/p/simrare/ SimRare] | [https://github.com/statgenetics/simrare now on github]
+
* [http://varianttools.sourceforge.net/Association/HomePage Variant Association Tools] | [https://github.com/vatlab/varianttools now on github]
+
* [[VMT|Variant Mendelian Tools]]
+
 
+
 
+
  
 
==[[Genetic Meetings of Interest]]==
 
==[[Genetic Meetings of Interest]]==
<!---
 
 
[[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