Changes

==Welcome to the Center for Statistical GeneticsTraining Resources==We are a an international group of statistical geneticists in [http://columbianeuroresearchwho wish to make training resources available to the genetics community.org/sergievsky/ The Gertrude H. Sergievsky Center] and [http://www.columbianeurology.org/ Department We offer tutorials for a variety of Neurology] at [https:analysis tools//www.ps.columbia.edu Columbia University Vagelos College of Physicians and Surgeons] in New York Citysoftware. We focus also offer courses on both the research and education of statistical genetics and a variety of topics related to analysis of human genetic epidemiologydata.

==Faculty=Our group===* Heather Cordell, Ph.D. (Newcastle University)* Andrew DeWan, Ph.D. (Yale University)* [[Suzanne_M_Leal_PhD|Suzanne M. Leal, Ph.D.]], Professor (Columbia University and DirectorRockefeller University)* [http://www.columbianeurology.org/profile/ischrauwen?profile=researcher Isabelle SchrauwenMichael Nothnagel, Ph.D.], Assistant Professor(University of Cologne)* [mailto:gw2411@cumc.columbia.edu Gao T. Wang, Ph.D.], Assistant Professor(Columbia University)

==Statistical Genetics Courses==[[Advgenemap2020|Advanced Gene Mapping Course]]<br Material on this site are open source and can be found on GitHub at https:/>January 27-31, 2020<br />The Rockefeller University, New York, USAgithub.com/statgenetics/statgen-courses

[[ComplexNGS2019|Complex Trait Analysis of Next Generation Sequence Data]]<br For questions concerning material on this site please raise them at the Discussion forum curated by our team, https:/>November 11/github.com/statgenetics/statgen-15, 2019<br courses/>Max Delbrück Center for Molecular Medicine, Berlin, Germanydiscussions

==Statistical Genetics SoftwareTutorials for Courses==* [[Tutorials#Annotation|ANNOVAR Annotation]] | [https://github.com/gaowstatgenetics/kbac KBACstatgen-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#FastLMM | Family-based Association using FaST-LMM, PLINK and R]] | [https://github.com/statgenetics/mendelprob MendelProbstatgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile]* and [https://codehub.googledocker.com/pr/phenomanstatisticalgenetics/ PhenoManfastlmm-gcta/tags docker image]* [[Tutorials#IGV|IGV]] | [https://github.com/statgenetics/phenoman now on githubstatgen-courses/blob/master/docker/igv.dockerfile dockerfile]* and [httphttps://bioinformaticshub.orgdocker.com/simpedr/rarestatisticalgenetics/ RarePedSimigv/tags docker image]* [[Tutorials#Gemini|Gemini]] | [https://github.com/statgenetics/rarepedsim now on githubstatgen-courses/blob/master/docker/gemini.dockerfile dockerfile]* and [httphttps://wwwhub.bioinformaticsdocker.orgcom/rv-gdtr/ RV-GDTstatisticalgenetics/gemini/tags docker image]* [[Tutorials#GCTA|GCTA]] | [https://github.com/statgenetics/rvstatgen-gdt now on github]* [http:courses/blob/bioinformatics.orgmaster/rv-tdtdocker/wiki/ RVfastlmm-TDTgcta.dockerfile dockefile] | and [https://githubhub.docker.com/statgeneticsr/rvstatisticalgenetics/fastlmm-gdt now on githubgcta/tags docker image]* [[Tutorials#GWAS:_Data_Quality_Control|GWAS: QC]] | [https://github.com/statgenetics/rvnpl RVstatgen-NPLcourses/blob/master/docker/plink.dockerfile dockerfile]* and [httphttps://wwwhub.bioinformaticsdocker.orgcom/seqlinkr/ SEQLinkagestatisticalgenetics/plink/tags docker image]* [[Tutorials#GWAS:_Association_Analysis_Controlling_for_Population_Substructure|GWAS: Controlling for Population Substructure]] | [https://github.com/gaowstatgenetics/SEQLinkage source on githubstatgen-courses/blob/master/docker/plink.dockerfile dockerfile]* and [httphttps://wwwhub.bioinformaticsdocker.orgcom/spowerr/start SEQPowerstatisticalgenetics/plink/tags docker image]* [[Tutorials#Epistasis_.28PLINK_and_CASSI.29 | Interaction analysis using PLINK and CASSI]] | [https://github.com/gaowstatgenetics/SEQPower source on githubstatgen-courses/blob/master/docker/epistasis.dockerfile dockerfile]* and [https://githubhub.docker.com/statgeneticsr/seqspark SEQSparkstatisticalgenetics/epistasis/tags docker image]* [http://bioinformatics[Tutorials#Linkage.org/simped SimPed2FFastLinkage|LINKAGE]] | [https://github.com/statgenetics/simped now on githubstatgen-courses/blob/master/docker/mlink.dockerfile dockerfile]* and [https://codehub.googledocker.com/pr/simrarestatisticalgenetics/ SimRaremlink/tags docker image]* [[Tutorials#Population_Genetics|Population Genetics]] | [https://github.com/statgenetics/simrare now on github]* [http:statgen-courses/blob/varianttools.sourceforge.netmaster/Associationdocker/HomePage Variant Association Toolspopgen.dockerfile dockefile] | and [https://githubhub.docker.com/vatlabr/varianttools now on githubstatisticalgenetics/popgen/tags docker image]* [[VMT|Variant Mendelian Tools]] ==Tutorials for Statistical Genetics Courses==* [[Tutorials#AnnotationPleiotropy|AnnotationPleiotropy]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pleiotropy.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/annovar pleiotropy/tags docker image]* [[Tutorials#Cochran_Armitage_Trend_TestPolygenic_risk_prediction_.28NPS_method.29|Cochran Armitage Trend TestPolygenic risk prediction using non-parametric shrinkage]]* [[Tutorials#GATK_and_IGV|GATK and IGV[https://github.com/statgenetics/statgen-courses/blob/master/docker/nps.dockerfile dockefile]and [https://hub.docker.com/r/statisticalgenetics/nps/tags docker image]* [[Tutorials#GenABELPSEQ|GenABELPLINK/SEQ (PSEQ)]]* | [[Tutorials#GWAShttps:_Data_Quality_Control|GWAS: QC//github.com/statgenetics/statgen-courses/blob/master/docker/pseq.dockerfile dockefile]]* and [[Tutorials#GWAShttps:_Association_Analysis_Controlling_for_Population_Substructure|GWAS: Controlling for Population Substructure]//hub.docker.com/r/statisticalgenetics/pseq/tags docker image]* [[Tutorials#Population_GeneticsR_and_PLINK|Population GeneticsR and PLINK exercise]]* | [https://github.com/statgenetics/statgen-courses/blob/master/docker/plink-r-nothnagel.dockerfile dockefile] and [Tutorials#PSEQ|PSEQ]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#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]* [[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]]-