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| | __NOTOC__ | | __NOTOC__ |
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| − | ==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. |
| | | | |
| − | Currently, we are located at 710 West 168th Street (Suzanne Leal and Isabelle Schrauwen), and 630 West 168th Street (Gao Wang).
| + | ===Our group=== |
| − | | + | * Heather Cordell, Ph.D. (Newcastle University) |
| − | On this website you will find research profiles of our faculty, trainees and visiting scholars, courses we teach and software we develop.
| + | * Andrew DeWan, Ph.D. (Yale University) |
| − | | + | * Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University) |
| − | : [[news|<span style="font-size: large; color: #800000;"> ☛ Read our news </span>]]
| + | * Michael Nothnagel, Ph.D. (University of Cologne) |
| − | : [[publications|<span style="font-size: large; color: #000000;"> ☛ List of publications </span>]]
| + | * Gao T. Wang, Ph.D. (Columbia University) |
| − | : [http://statgen.us/lab-wiki/project_resource <span style="font-size: large; color: #000000;"> ☛ List of projects (complex traits) </span>]
| + | |
| − | | + | |
| − | ==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==
| + | |
| − | ===Current members===
| + | |
| − | * Anushree Acharya, Research Assistant (Mendelian Genetics)
| + | |
| − | * Shikha Asrani, Master student (Computer Science)
| + | |
| − | * Thashi Bharadwaj, Postdoc Researcher
| + | |
| − | * Alexis Bryan, Master student (Epidemiology)
| + | |
| − | * Diana Cornejo, Postdoc Researcher
| + | |
| − | * Jenna Everard, Undergraduate student (Environmental Biology and Computer Science)
| + | |
| − | * Tabassum Fabiha, Undergraduate student (Computer Science) | + | |
| − | * Samantha Figueredo, Undergraduate student (Computer Science)
| + | |
| − | * Xinqi Li, Master Student (Computer Science)
| + | |
| − | * Nicole Lin, Undergraduate student (Engineering)
| + | |
| − | * Sibei Liu, Master Student (Biostatistics)
| + | |
| − | * Asvin Jagadeesan (AJ), Undergraduate Student (Computer Science)
| + | |
| − | * Magda Kamila Kadlubowska, Undergraduate student (Computer science)
| + | |
| − | * Yuqi Miao, Master Student (Biostatistics)
| + | |
| − | * Liz M Nouel, Research Assistant (Mendelian Genetics)
| + | |
| − | * [https://www.linkedin.com/in/anmol-singh-4211839a/ Anmol Singh], Master Student (Biostatistics)
| + | |
| − | * Haoyue Shuai, Master Research Assistant (Bioinformatics) | + | |
| − | * Hao Sun, Master Student (Biostatistics)
| + | |
| − | * Ran Wang, Master Student (Epidemiology)
| + | |
| − | | + | |
| − | Note: the list of current members does not include rotation students.
| + | |
| − | | + | |
| − | ===Alumni===
| + | |
| − | Please find [[alumni|on this page]] previous personnel, visiting scholars and rotation students.
| + | |
| | | | |
| | ==Statistical Genetics Courses== | | ==Statistical Genetics Courses== |
| − | [[Advgenemap2021|Advanced Gene Mapping]] <br /> January 25-29, 2021<br />The Rockefeller University, New York, USA | + | '''[[Advgenemap2026|Advanced Gene Mapping]]'''<br />(January 11-15 2027) tenative<br />The Rockefeller University, New York, USA |
| | | | |
| − | [[Genassoc2021|Genetic Association]] (Cancelled due to COVID19 restrictions)<br />September 13-17, 2021 <br />Max Delbrück Center for Molecular Medicine, Berlin, Germany | + | '''[[GABeyond2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]'''<br />September 14-18, 2026 <br />The Max Delbrück Center, Berlin, Germany |
| − | | + | |
| − | [[ComplexNGS2021|Complex Trait Analysis of Next Generation Sequence Data]]<br />November 22-26, 2021<br />Max Delbrück Center for Molecular Medicine, Berlin, Germany
| + | |
| − | | + | |
| − | [[Previous_Courses|Previous Course Pages]]
| + | |
| | | | |
| | ==Tutorials for Courses== | | ==Tutorials for Courses== |
| − | * [[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#FastLMM_&_GCTA|FastLMM & GCTA]] |
| − | * [[Tutorials#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
| + | * [[Tutorials#Mendelian Randomization|Mendelian Randomization]] |
| − | * [[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#Pleiotropy|Pleiotropy]] |
| − | * [[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#PLINK_GWAS:_Data_Quality_Control_and Association_Analysis_Controlling_for_Population_Substructure|PLINK GWAS: QC and Controlling for Population Substructure]] |
| − | * [[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#Power_Analysis|Power Analysis]] |
| − | * [[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] | + | * [[Tutorials#REGENIE|REGENIE]] |
| − | * [[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#Regression_and_Intro_to_PLINK_and_R|Regression and Intro to PLINK and R]] |
| − | * [[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#Pencil_and_Paper_Exercise|Pencil and Paper Exercise]] |
| − | * [[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#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#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#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|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#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#SEQLinkage|SEQLinkage]]
| + | |
| − | * [[Tutorials#SEQSpark|SEQSpark]]
| + | |
| − | * [[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]]
| + | |
| − | -->
| + | |
| − | ==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 |
| | | | |
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.
