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Advgenemap2021

1,516 bytes added, 18:03, 29 January 2021
/* Shamil Sunyaev */
==Course Instructors==
The instructors for the course are Heather Cordell (University of Newcastle), Nancy Cox (Vanderbilt University), Andrew DeWan (Yale University), Suzanne Leal (The Rockefeller University & Columbia University), [http://www.fas.harvard.edu/~biophys/Shamil_Sunyaev.htm Shamil Sunyaev] (Harvard University) & Gao Wang (Columbia University). Judy Matuk (HRP Consulting Group) will lecture on ethics and the regulation of human subject research. A special guest lecture will be given by Jurg Ott (Rockefeller University).
==Additional Information==
[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==
====[//www.statgen.us/files/2020/01/docs/lectures/Lecture_booklet.pdf All Lectures]====
====[//www.statgen.us/files/2020/01/docs/exercises/Booklet_exercises.pdf All Exercises]====
===Heather Cordell===
[http://www.statgen.us/files/2021/02/bios/about_HJC.pdf About Heather Cordell]
 
====Lectures====
* [http://www.statgen.us/files/20202021/01/docs02/lectures/NY2020NY2021-lecture1-nopause_4nopause.pdf Genome-wide association studies (GWAS) - Part 1]* [http://www.statgen.us/files/2020/012021/docs02/lectures/NY2020NY2021-lecture2-nopause_4nopause.pdf Genome-wide association studies (GWAS) - Part 2]
====Exercises====
* [[Tutorials#FastLMM | http://statgen.us/files/2021/02/exercises/FASTLMM-NY2020.pdf Family-based Association using FaST-LMM, PLINK and R]] | * [httpshttp://githubstatgen.comus/statgeneticsfiles/statgen-courses2021/blob02/masterexercises/docker/fastlmmGCTA-gctaNY2021.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker imagepdf GCTA]* [[Tutorials#GCTA|GCTA]] | [httpshttp://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https:us/files/hub.docker.com2021/r02/statisticalgeneticsexercises/fastlmmEpistasis-gcta/tags docker image]* [[Tutorials#Epistasis_NY2020.28PLINK_and_CASSI.29 | 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]
===Nancy Cox===
[http://statgen.us/files/2021/02/bios/about_njc.pdf about Nancy Cox]
 
====Lectures====
* [http://www.statgen.us/files/2020/012021/docs02/lectures/LealCourse_Cox_Jan2020LealCourse_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] ====LecturesLecture====* [http://www.statgen.us/files/20202021/02/lectures/DeWan_Adv_Gene_Mapping_Mendelian%20Randomization.pdf Mendelian randomization]* [http://statgen.us/files/012021/docs02/lectures/Rockefeller_Adv_Course_DeWan_pleiotropy_4Rockefeller_Adv_Course_DeWan_pleiotropy.pdf From cross-phenotype associations to pleiotropy in human genetic studiesPleiotropy]
====Exercises====
* [[Tutorials#Pleiotropy|http://statgen.us/files/2021/02/exercises/pleio_exercise.pdf Pleiotropy]] | * [httpshttp://githubstatgen.comus/files/2021/02/exercises/pleio_exercise_answers.pdf Answers to Pleitropy Exercise]* [http:/statgenetics/statgen-courses.us/blobfiles/master2021/docker02/pleiotropyexercises/MR_exercise.dockerfile dockefilepdf Mendelian Randomization] and * [httpshttp://hubwww.dockerstatgen.comus/rfiles/statisticalgenetics2021/pleiotropy02/tags docker imageexercises/MR_exercise_answers.pdf Mendelian Randomization Answers]
===Suzanne Leal===
[http://www.statgen.us/files/2021/02/bios/about_sml.pdf About Suzanne Leal]
 
====Lectures====
* [http://www.statgen.us/files/2020/012021/docs02/lectures/data_quality_control_1.pdf Data Quality Control]* [http://www.statgen.us/files/20202021/01/docs02/lectures/NGS_data_qc.pdf NGS Data Quality Control]* [http://www.statgen.us/files/20202021/01/docs02/lectures/analysis_rare_variants_part_1.pdf Complex Trait Association Analysis of Rare VariantsObtained from Sequence Data: Population-Based Data]* [http://www.statgen.us/files/2020/012021/docs02/lectures/power_sample_sizes.pdf Power Analysis for Single 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)]] | [httpshttp://githubstatgen.comus/statgeneticsfiles/statgen-courses2021/blob02/masterexercises/docker/pseqPSEQ_exercise.dockerfile dockefilepdf PLINK/SEQ (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]] | * [httpshttp://githubstatgen.comus/statgeneticsfiles/statgen-courses2021/blob02/masterexercises/docker/vatArmitage_sample_size.dockerfile dockerfilepdf Cochran Armitage Trend Test for GWAS power analysis] and * [httpshttp://hub.dockerstatgen.comus/rfiles/statisticalgenetics2021/vat02/tags docker imageexercises/FunctionalAnnotation.2021.pdf ANNOVAR Annotation]* [[Tutorials#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test http://statgen.us/files/2021/02/exercises/GWAS_Data_Controlling_for_Substructure_V2.pdf Genome-Wide Association - Association Analysis Controlling for GWAS power analysis]Population Substructure]* [http://statgen.us/files/2021/02/exercises/PLINK_data_QC_V2.pdf Genome-Wide Association Analysis - Data Quality Control] ===Judy Matuk===[Tutorials#Annotation|ANNOVAR Annotation]http://www.statgen.us/files/2021/02/bios/about_jm.pdf About Judy Matuk] |  ====Lectures====* [httpshttp://githubstatgen.comus/statgeneticsfiles/2021/02/lectures/Rockefeller_draft_HSR%20Ethics%20and%20Regulations%20PPT_%20jm%201.18.2021.pdf Human Subject Training] ===Jurg Ott===[http://www.statgen-courses.us/blobfiles/master2021/docker02/annovarbios/about_jo.dockerfile dockefilepdf About Jurg Ott] and  ====Lectures====[httpshttp://hubwww.dockerstatgen.comus/rfiles/statisticalgenetics2021/annovar02/tags docker imagelectures/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]
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* [[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 dockerfile] and [https://hub.docker.com/r/statisticalgenetics/nps/tags docker image]
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This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI)====Lectures====* [http://statgen.us/files/2021/02/lectures/Rockefeller_complex_traits_2021.pdf Complex Traits]* [http://statgen.us/files/2021/02/lectures/Rockefeller_functional_annotation_2021.pdf Functional Annotation]* [http://statgen.us/files/2021/02/lectures/Rockefeller_polygenic_risk_score_2021.pdf Polygenic Risk Score]* [http://statgen.us/files/2021/02/lectures/Rockefeller_population_genetics_2021.pdf Population Genetics]
===Gao Wang===
[http://www.statgen.us/files/2021/02/bios/about_gw.pdf 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]
===Heather Cordell=Exercises=====Nancy Cox===* [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). ===Andrew DeWanDan Zhou===[http://www.statgen.us/files/2021/02/bios/about_dz.pdf About Dan Zhou]===Suzanne Leal=Computer Demonstration=====Shamil Sunyaev======Gao Wang===* [http://statgen.us/files/2021/02/lectures/MR-JTI.pdf MR-JTI: a framework for Joint Tissue Imputation-based TWAS and Mendelian Randomization]
Bureaucrat, administrator
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