Changes
From Statistical Genetics Courses
/* Handouts */
For additional information on scientific program contact the course organizer [mailto:suzannemleal@gmail.com?subject=Rockefeller Advanced Gene Mapping Course 2020 Suzanne Leal]: <br />email: [mailto:suzannemleal@gmail.com suzannemleal@gmail.com] or [mailto:sml3@cumc.columbia.edu sml3@cumc.columbia.edu] <br />Tel: +1 (212) 304-7047
==Course Photo==
[[File:142FBA93-B26F-45A4-A0C5-264B812AB558.JPG|thumb|none|]]
====Exercises====* [[Tutorials#FastLMM | Family-based Association using FaST-LMM, PLINK and R]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.usdockerfile dockefile] and [https:/files/2020hub.docker.com/01r/Application%20Advanced%20Gene%20Mapping%20Course%202020–%20New%20Yorkstatisticalgenetics/fastlmm-gcta/tags docker image]* [[Tutorials#GCTA|GCTA]] | [https://github.html Click here for application formcom/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/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]
===Nancy Cox=======Lectures====* [//www.statgen.us/files/2020/01/Rockefeller_advanced_course_flyer_2020docs/lectures/LealCourse_Cox_Jan2020.pdf Click here for course flyerIntegrative Approaches in Biobanks: Getting to Biological Mechanisms of Disease] – Please Post and Distribute
===Andrew DeWan=======Lectures====* [//www.statgen.us/files/2020/01/adv_gene_mapping_schedule_2020docs/lectures/Rockefeller_Adv_Course_DeWan_pleiotropy_4.pdf Click here From cross-phenotype associations to pleiotropy in human genetic studies] ====Exercises====* [[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] ===Suzanne Leal=======Lectures====* [//www.statgen.us/files/2020/01/docs/lectures/data_quality_control_1.pdf Data Quality Control]* [//www.statgen.us/files/2020/01/docs/lectures/NGS_data_qc.pdf NGS Data Quality Control]* [//www.statgen.us/files/2020/01/docs/lectures/analysis_rare_variants_part_1.pdf Complex Trait Association Analysis of Rare Variants]* [//www.statgen.us/files/2020/01/docs/lectures/power_sample_sizes.pdf Power Analysis for course scheduleSingle and Rare Variant Aggregate Association Analyses]* [//www.statgen.us/files/2020/01/docs/lectures/Analysis_rare_variants_part_2.pdf National Heart Lung and Blood Institute Exome Sequencing Project] ====Exercises====* [[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#Variant_Association_Tools|Association Analysis of Sequence Data using Variant Association Tools for Complex Traits]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/vat.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/vat/tags docker image]* [[Tutorials#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]* [[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] ===Bogdan Pasanuic=======Lectures====* [//www.statgen.us/files/2020/01/docs/lectures/finemapping_pasaniuc.pdf Statistical fine-mapping of GWAS signals]<!--====Exercises====* finemap--> ===Shamil Sunyaev=======Lectures====* [//www.statgen.us/files/2020/01/docs/lectures/Rockefeller_pop_gen_2020.pdf Population Genetics]* [//www.statgen.us/files/2020/01/docs/lectures/Rockefeller_complex_traits_2020.pdf Evolution, maintenance and allelic architecture of complex traits]* [//www.statgen.us/files/2020/01/docs/lectures/Rockefeller_polygenic_2020.pdf Polygenic Risk Score]* [//www.statgen.us/files/2020/01/docs/lectures/Rockefeller_function_2019.pdf Functional Annotation] ====Exercises====* [[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]
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).
