About
These are materials for workshop held at the University of Tokyo on 12-15th November 2018. The main website for this workshop is found here with thanks to Hiromi Kanegae from Graduate School of Agricultural and Life Sciences, University of Tokyo for setting it up.
Lecturers
Gota Morota (GM) Virginia Polytechnic Institute and State University, USA
Diego Jarquin (DJ) University of Nebraska-Lincoln, USA
Emi Tanaka (ET) University of Sydney, Australia
Malachy Campbell (MC) University of Nebraska-Lincoln, USA
Jessica Tressou (JT) INRA, France
Hiroyoshi Iwata (HI) University of Tokyo, Japan
Schedule
Day 1
9:00-10:10: Basic statistical computing in R (MC) - R Markdown
10:10-10:20: Break
10:20-12:00: Data visualization in R (ET) - ggplot2 + desplot
12:00-13:00: Lunch
13:00-14:00 Introduction to Quantitative Genetics (GM)
14:00-14:10: Break
14:10-15:40: Least squares and Linear mixed model (MC, JT)
15:40-15:50: Break
15:50-16:50 Bayesian methods (JT)
17:30-19:30 Social mixer @ YAYOI AUDITORIUM - ANNEX ¥5,000
Day 2
9:00-9:30 Genomic heritability (MC, GM)
9:30-9:40 Break
9:40-12:00 GWAS (HI)
12:00-13:00 Lunch
13:00-14:00 GBLUP and RR-BLUP (MC, GM)
14:00-15:00 Bayesian alphabet (DJ)
15:00-15:10 Break
15:10-16:10 Classical GxE including FW, AMMI, and biplot (HI, DJ)
16:10-17:10 GxE covariates (HI, DJ)
Day 3
9:00-11:00 Introduction to ASReml (ET)
11:00-11:10 Break
11:10-12:00 Theoretical part of factor analytic model (ET)
12:00-13:00 Lunch
13:00-14:00 Application of factor analytic model to GxE analysis with ASReml (ET)
14:00-14:10 Break
14:10-15:10: Bayesian factor analytic model (DJ, GM)
15:10-15:20: Break
15:20-16:20 Spatial analysis (ET) Gilmour et al. (1997)
16:20-17:00 Introduction to R-INLA (JT)
Day 4
9:00-12:00 Multi-trait methods for GWAS and GP (HI, DJ, GM)
12:00-13:00 Lunch
13:00-15:00 Bayesian network (MC, GM)
15:00-15:10 Break
15:10-17:00 Experimental design + Optimal designs (ET)