Armidale Animal Breeding Summer Course 2015

Venue: University of New England, Armidale, NSW Australia

Course Audience: Postgraduate students and other professionals

Module 1

Primer to Analysis of Genomic Data Using R

Teacher: Cedric Gondro

University of New England

Armidale, , Australia

Dates: Wednesday 28 January 2015 (9am) - Friday 30 January 2015 (4pm)

· Content Module 1

Website Link for materials Module 1:

http://cgondro2.une.edu.au/Rcourse.htm

Module 2

From Sequence Data to Genomic Prediction

Teachers: Ben Hayes and Hans Daetwyler

Department of Environment and Primary Industries

Bundoora, Victoria, Australia

Dates: Monday 2 February 2015 (9am) - Friday 6 February 2015 (4pm)

Materials Module 2:

NOTES

Course Notes

SLIDES

Day1 Intro

Day1 Sequence

Day2 Imputation

Day 3 GWAS

Day 4 Genomic Prediction

Day5 Genomic Prediction with Sequence

Day5 Genomic Breeding Programs

Day5 Imputation to sequence (1 slide)

http://jvanderw.une.edu.au/aabc_materials2015.htm

PRACTICALS

Manual

325_bulls_gens.txt

map_10_markers.txt

reference_50.txt

reference_map_50.txt

target_50.txt

target_true.txt

xvec_day4.inp

xvec_prog.inp

yvec_day4.inp

yvec_prog.inp

xvecday5.inp

yvecday5.inp

data for sequence prac (100 Mb) is on

https://www.dropbox.com/sh/3ug96im9vyxlo7f/AAB5eOUyQGXhkYcPa6ss_NrAa

Material of previous years:

Armidale Animal Breeding Summer Course 2014   Materials

Breeding Program Design with Genomic Selection: Jack Dekkers, Julius van der Werf

Armidale Animal Breeding Summer Course 2012   Materials

Statistical Methods for Genome-Enabled Selection: Daniel Gianola, Gustavo de los Campos

Armidale Animal Breeding Summer Course 2011   Materials

· Statistical methods and design in plant breeding and genomics: Ian Mackay

· IBD inference in genome association studies: Elizabeth Thompson

Armidale Animal Breeding Summer Course 2010   Materials

· Application of evolutionary algorithms to solve complex problems in quantitative genetics

and bioinformatics: Brian Kinghorn, Cedric Gondro

· Bayesian methods in genome association studies: Dorian Garrick,  Rohan Fernando

Armidale Animal Breeding Summer Course 2009   Materials

· Quantitative Genetic Theory and Analysis- Selection Theory:    Bruce Walsh

· Quantitative Genetic Models for social interaction and inherited variability: Piter Bijma

Armidale Animal Breeding Summer Course 2008   Materials 

· Genomic Selection:       Ben Hayes

Armidale Animal Breeding Summer Course 2007   Materials

· Generalized Linear Mixed Models:        Steve Kachman

Armidale Animal Breeding Summer Course 2006    Materials

· Gene Expression:          Toni Reverter

· Breeding Program Design:         Graser, James, Van der Werf

Armidale Animal Breeding Summer Course 2005 Materials

· Breeding Objectives: Gibson, Van der Werf, Kinghorn

· Scientific Writing:          David Lindsay

· ASReml:           Arthur Gilmour

Armidale Animal Breeding Summer Course 2004 Materials

· Bayesian for Beginners               Kerrie Mengersen

· Bayesian Models for QTL analysis        Michel Perez-Enciso

· Bioinformatics   John McEwan

Armidale Animal Breeding Summer Course 2003    Materials

· Scientific Writing:  David Lindsay

· Linear Models for animal breeding:   Julius van der Werf, Mike Goddard

· QTL mapping for practitioners, from linkage to gene: Ben Hayes, Julius van der Werf

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