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Advgenemap2021

239 bytes removed, 18:03, 29 January 2021
/* Shamil Sunyaev */
[http://statgen.us/files/2021/02/Rockefeller_advanced_course_flyer_2021.pdf Click here for course flyer] (please post and distribute)
===[https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials How to run the exercises]===
==Handouts==
 
===Heather Cordell===
[http://www.statgen.us/files/2021/02/bios/about_HJC.pdf About Heather Cordell]
====Lectures====
====Exercises====
* [http://statgen.us/files/2021/02/exercises/FASTLMM-NY2020.pdf Family-based Association using FaST-LMM, PLINK and R] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image]* [http://statgen.us/files/2021/02/exercises/GCTA-NY2021.pdf GCTA] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image]* [http://statgen.us/files/2021/02/exercises/Epistasis-NY2020.pdf 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#FastLMM | Family-based Association using FaST-LMM, PLINK and R]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image]
* [[Tutorials#GCTA|GCTA]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockerfile] 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===
[http://statgen.us/files/2021/02/bios/about_njc.pdf about Nancy Cox]
 
====Lectures====
[http://statgen.us/files/2021/02/lectures/LealCourse_Cox_Jan2021.pdf Integrative Approaches in Biobanks: Getting to Biological Mechanisms of Disease]
===Andrew DeWan===
[http://www.statgen.us/files/2021/02/bios/about_atd.pdf About Andy DeWan]
====Lecture====
* [http://statgen.us/files/2021/02/lectures/DeWan_Adv_Gene_Mapping_Mendelian%20Randomization.pdf Mendelian randomization]
* [http://statgen.us/files/2021/02/lectures/Rockefeller_Adv_Course_DeWan_pleiotropy.pdf Pleiotropy]
====Exercises====
* [http://statgen.us/files/2021/02/exercises/pleio_exercise.pdf Pleiotropy] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pleiotropy.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/pleiotropy/tags docker image]* [http://statgen.us/files/2021/02/exercises/pleio_exercise_answers.pdf. Answers to Pleitropy Exercise]
* [http://statgen.us/files/2021/02/exercises/MR_exercise.pdf Mendelian Randomization]
 <!--* [[Tutorials#Pleiotropy|Pleiotropy]] | [httpshttp://githubwww.com/statgenetics/statgen-courses.us/blobfiles/master2021/docker02/pleiotropy.dockerfile dockerfile] and [https:exercises//hubMR_exercise_answers.docker.com/r/statisticalgenetics/pleiotropy/tags docker imagepdf Mendelian Randomization Answers]-->
===Suzanne Leal===
[http://www.statgen.us/files/2021/02/bios/about_sml.pdf About Suzanne Leal]
 
====Lectures====
* [http://statgen.us/files/2021/02/lectures/data_quality_control_1.pdf Data Quality Control]
* [http://statgen.us/files/2021/02/lectures/NGS_data_qc.pdf NGS Data Quality Control]
* [http://statgen.us/files/2021/02/lectures/analysis_rare_variants_part_1.pdf Complex Trait Association Analysis of Rare Variants Obtained from Sequence Data: Population-Based Data]
* [http://statgen.us/files/2021/02/lectures/power_sample_sizes.pdf Power Analysis for Single and Rare Variant Aggregate Association Analyses]
====Exercises====
* [[Tutorials#PSEQ|PLINK/SEQ (PSEQ)]] | [httpshttp://githubstatgen.comus/statgeneticsfiles/statgen-courses2021/blob02/masterexercises/dockerPSEQ_exercise.pdf PLINK/pseq.dockerfile dockerfileSEQ (PSEQ)] and * [httpshttp://hub.dockerstatgen.comus/rfiles/statisticalgenetics2021/pseq02/tags docker image]* [[Tutorials#Variant_Association_Tools|exercises/VAT_2021.pdf 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]
* [http://statgen.us/files/2021/02/exercises/Armitage_sample_size.pdf Cochran Armitage Trend Test for GWAS power analysis]
* [http://statgen.us/files/2021/02/exercises/FunctionalAnnotation.2021.pdf ANNOVAR Annotation] | * [httpshttp://githubstatgen.comus/statgeneticsfiles/statgen-courses2021/blob02/masterexercises/docker/annovarGWAS_Data_Controlling_for_Substructure_V2.dockerfile dockerfilepdf Genome-Wide Association - Association Analysis Controlling for Population Substructure] and * [httpshttp://hubstatgen.docker.comus/rfiles/statisticalgenetics2021/annovar02/tags docker imageexercises/PLINK_data_QC_V2.pdf Genome-Wide Association Analysis - Data Quality Control]
<!--
* [[Tutorials#PSEQ|PLINK/SEQ (PSEQ)]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pseq.dockerfile dockerfile] 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]]
* [http://statgen.us/files/2021/02/exercises/FunctionalAnnotation.2021.pdf ANNOVAR Annotation] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/annovar.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/annovar/tags docker image]
-->
===Judy Matuk===
[http://www.statgen.us/files/2021/02/bios/about_jm.pdf About Judy Matuk]
====Lectures====
* [http://statgen.us/files/2021/02/lectures/Rockefeller_draft_HSR%20Ethics%20and%20Regulations%20PPT_%20jm%201.18.2021.pdf Human Subject Training]
 
===Jurg Ott===
[http://www.statgen.us/files/2021/02/bios/about_jo.pdf About Jurg Ott]
 
====Lectures====
[http://www.statgen.us/files/2021/02/lectures/FPMforInteractions2021-01.pptx Frequent Pattern Mining Methods for Finding SNP-SNP Interactions]
===Shamil Sunyaev===
[http://www.statgen.us/files/2021/02/bios/about_ss.pdf About Shamil Sunyaev]
 
====Exercises====
* [http://statgen.us/files/2021/02/exercises/NPS.pdf Polygenic risk prediction using non-parametric shrinkage] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/nps.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/nps/tags docker image]
<!--====Lectures====* [[Tutorials#Polygenic_risk_prediction_http://statgen.28NPS_methodus/files/2021/02/lectures/Rockefeller_complex_traits_2021.29|Polygenic risk prediction using non-parametric shrinkagepdf Complex Traits]] | * [httpshttp://githubstatgen.comus/files/2021/02/lectures/Rockefeller_functional_annotation_2021.pdf Functional Annotation]* [http:/statgenetics/statgen-courses.us/blobfiles/master2021/docker02/npslectures/Rockefeller_polygenic_risk_score_2021.dockerfile dockerfilepdf Polygenic Risk Score] and * [httpshttp://hub.dockerstatgen.comus/rfiles/statisticalgenetics2021/nps02/tags docker imagelectures/Rockefeller_population_genetics_2021.pdf Population Genetics]-->
===Gao Wang===
====Exercises====* [httpshttp://githubwww.com/statgenetics/statgen-courses/raw/master/handout/finemapping.pdf Statistical fine-mapping in association studies] | [https:us/files/github.com2021/statgenetics02/statgen-coursesbios/blob/master/docker/finemapabout_gw.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/finemap/tags docker imagepdf About Gao Wang]
====Lectures====
* [http://statgen.us/files/2021/02/lectures/Lecture_Univariate_Fine_Mapping.pdf Statistical fine-mapping]
* [http://statgen.us/files/2021/02/lectures/Lecture_Multivariate_Analysis.pdf Multivariate analysis]
 
====Exercises====
* [https://github.com/statgenetics/statgen-courses/raw/master/handout/finemapping.docx Statistical fine-mapping in association studies] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/finemap.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/finemap/tags docker image]
* [https://github.com/statgenetics/statgen-courses/raw/master/handout/finemapping_answers.docx Answers to fine-mapping exercise questions]
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).
 
===Dan Zhou===
[http://www.statgen.us/files/2021/02/bios/about_dz.pdf About Dan Zhou]
====Computer Demonstration====
* [http://statgen.us/files/2021/02/lectures/MR-JTI.pdf MR-JTI: a framework for Joint Tissue Imputation-based TWAS and Mendelian Randomization]
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