[R-sig-genetics] UK.GeneticDataAnalysisUsingR.ThibautJombart.23-27Oct.

Thu Mar 23 11:43:45 CET 2017

"Genetic data analysis/exploration using R" (GDAR03)

This course will be delivered by Dr. Thibaut Jombart who authors the
adegenet package and Dr. Zhian Kamvar.

This course will run from the 23rd - 27th October at Margam discovery 
centre
in Wales, United Kingdom.

Course Overview:
This course provides a comprehensive introduction to exploratory
statistical methods used in population genetics and molecular ecology.
Participants will become proficient in a range of approaches for 
uncovering
genetic structures from usual genetic data including most genetic 
markers
(e.g. microsatellites, SNPs, AFLP) and genetic sequences (DNA or amino-
acid). After covering different types of phylogenetic reconstruction, 
and
basic population genetics tests, a strong emphasis will be put on using
factorial methods (e.g. Principal Component Analysis) for investigating
genetic diversity. In particular, we will focus on the identification 
and
description of genetic clusters, and on characterising spatial genetic
patterns. The last day of the course will be an open problem day, where
participants will be able to analyse their own data.

Day 1
Intro to phylogenetic reconstruction.
Module 1a: Reconstructing phylogenies from genetic sequence data. Three
main approaches covered: distance-based phylogenies; maximum parsimony; 
and
likelihood-based approaches.
Module 1b: Short R refresher.
Practical 1: Phylogenetic reconstruction using R. Three main approaches
plus rooting a tree; assessing/testing for a molecular clock; and
bootstrapping.
Main packages: ape, phangorn.

Day 2
Intro to multivariate analysis of genetic data
Module 2: Key concepts in multivariate analysis. Focus on using 
factorial
methods for genetic data analysis.
Practical 2: Basics of multivariate analysis of genetic data in R. 
Topics
include: data handling, population genetic tests of population structure
(PCA, PCoA).
Main packages: adegenet, ade4, ape.

Day 3
Exploring group diversity
Module 3: Approaches to identifying and describing genetic clusters. 
Topics
include: hierarchical clustering, K-means, population-level multivariate
analysis (between-group-PCA, DA, DAPC).
Practical 3: Applying the approaches covered in morning lecture and
emphasising their strengths and weaknesses.
Main packages: adegenet, ade4.

Day 4
Spatial genetic structures
Module 4: Discussing the origin and significance of spatial genetic
patterns, and how to test for them.
Practical 4: Visualising and analysing spatial genetic data. Topics:
spatial density estimates, Moran/Mantel tests, mapping principal 
components
in PCA, spatial PCA.
Main packages: adegenet, adehabitat, ade4.

Day 5
Using R for reproducible science.
Module 5: Using R for reproducible science
Practical 5: Practical session based on morning lecture
Main packages: knitr, Sweave, rmarkdown

If you have any questions please email oliverhooker at prstatistics.com or
visit www.prstatistics.com

To book online go to http://www.prstatistics.com/course/genetic-data-
analysis-exploration-using-r-gdar03/

Other up-coming courses are as follows

1.	ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R 
#MVSP
3rd – 7th April 2017, Scotland, Prof. Pierre Legendre, Dr. Olivier 
Gauthier
http://www.prstatistics.com/course/advances-in-spatial-analysis-of-multivariate-ecological-data-theory-and-practice-mvsp02/

2.	ADVANCING IN STATISTICAL MODELLING FOR EVOLUTIONARY BIOLOGISTS AND 
ECOLOGISTS USING R #ADVR
17th – 21st April 2017, Scotland, Dr. Luc Bussiere, Dr. Ane Timenes 
Laugen
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr06/

3.	CODING, DATA MANAGEMENT AND SHINY APPLICATIONS USING RSTUDIO FOR 
EVOLUTIONARY BIOLOGISTS AND ECOLOGISTS #CDSR
15th - 19th May, Scotland Dr. Aline Quadros
http://www.prstatistics.com/course/coding-data-management-and-shiny-applications-using-rstudio-for-evolutionary-biologists-and-ecologists-cdsr01/

4.	GEOMETRIC MORPHOMETRICS USING R #GMMR
5th – 9th June 2017, Scotland, Prof. Dean Adams, Prof. Michael 
Collyer, Dr. Antigoni Kaliontzopoulou
http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/

5.	MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA #MASE
19th – 23rd June, Canada, Prof. Subhash Lele, Dr. Peter Solymos
http://www.prstatistics.com/course/multivariate-analysis-of-spatial-ecological-data-using-r-mase01/

6.	TIME SERIES MODELS FOR ECOLOGISTS USING R (JUNE 2017 #TSME
26th – 30th June, Canada, Dr. Andrew Parnell
http://www.prstatistics.com/course/time-series-models-foe-ecologists-tsme01/

7.	BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS #BIGB
3rd – 7th July 2017, Scotland, Dr. Nic Blouin, Dr. Ian Misner
http://www.prstatistics.com/course/bioinformatics-for-geneticists-and-biologists-bigb02/

8.	META-ANALYSIS IN ECOLOGY, EVOLUTION AND ENVIRONMENTAL SCIENCES 
#METR01
24th – 28th July, Scotland, Prof. Julia Koricheva, Prof. Elena 
Kulinskaya
http://www.prstatistics.com/course/meta-analysis-in-ecology-evolution-and-environmental-sciences-metr01/

9.	SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R #SPAE
7th – 12th August 2017, Scotland, Prof. Jason Matthiopoulos, Dr. James 
Grecian
http://www.prstatistics.com/course/spatial-analysis-ecological-data-using-r-spae05/

10.	ECOLOGICAL NICHE MODELLING USING R #ENMR
16th – 20th October 2017, Scotland, Dr. Neftali Sillero
http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr01/

11.	INTRODUCTION TO BIOINFORMATICS USING LINUX #IBUL
16th – 20th October, Scotland, Dr. Martin Jones
http://www.prstatistics.com/course/introduction-to-bioinformatics-using-linux-ibul02/

12.	GENETIC DATA ANALYSIS AND EXPLORATION USING R #GDAR
23rd – 27th October, Wales, Dr. Thibaut Jombart, Zhian Kavar
http://www.prstatistics.com/course/genetic-data-analysis-exploration-using-r-gdar03/

13.	STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY 
BIOLOGISTS USING R #SEMR
23rd – 27th October, Wales, Prof Jarrett Byrnes, Dr. Jon Lefcheck
http://www.prstatistics.com/course/structural-equation-modelling-for-ecologists-and-evolutionary-biologists-semr01/

14.	LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R #LNDG
6th – 10th November, Wales, Prof. Rodney Dyer
http://www.prstatistics.com/course/landscape-genetic-data-analysis-using-r-lndg02/

15.	APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS #ABME
20th - 25th November 2017, Scotland, Prof. Jason Matthiopoulos, Dr. Matt 
Denwood
http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists-epidemiologists-abme03/

16.	INTRODUCTION REMOTE SENSING AND GIS APPLICATIONS FOR ECOLOGISTS 
#IRMS
27th Nov – 1st Dec, Wales, Dr Duccio Rocchini, Dr. Luca Delucchi
http://www.prstatistics.com/course/introduction-to-remote-sensing-and-gis-for-ecological-applications-irms01/

17.	INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB
27th Nov – 1st Dec, Wales, Dr. Martin Jones
http://www.prstatistics.com/course/introduction-to-python-for-biologists-ipyb04/

18.	DATA VISUALISATION AND MANIPULATION USING PYTHON #DVMP
11th – 15th December 2017, Wales, Dr. Martin Jones
http://www.prstatistics.com/course/data-visualisation-and-manipulation-using-python-dvmp01/

19.	ADVANCING IN STATISTICAL MODELLING USING R #ADVR
11th – 15th December 2017, Wales, Dr. Luc Bussiere, Dr. Tom Houslay, 
Dr. Ane Timenes Laugen,
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr07/

20.	INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING #IBHM
29th Jan – 2nd Feb 2018, Scotland, Dr. Andrew Parnell
http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm02/

21.	ANIMAL MOVEMENT ECOLOGY (February 2018) #ANME
??th - ??th February 2018, Wales, Dr Luca Borger, Dr. John Fieberg

22.	AQUATIC TELEMENTRY DATA ANALYSIS USIR R (TBC) #ATDAR
??th - ??th February 2018, Wales,

23.	FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND 
COMPUTATION #FEER
5th – 9th March 2018, Scotland, Dr. Francesco de Bello, Dr. Lars 
Götzenberger, Dr. Carlos Carmona
http://www.prstatistics.com/course/functional-ecology-from-organism-to-ecosystem-theory-and-computation-feer01/

24.	STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM
Dr. Andrew Parnell, Dr. Andrew Jackson – Date and location to be 
confirmed

25.	NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA
Dr. Marco Scotti - Date and location to be confirmed

26.	MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV0
Prof David Warton - Date and location to be confirmed

27.	ADVANCED PYTHON FOR BIOLOGISTS #APYB
Dr. Martin Jones - Date and location to be confirmed

28.	PHYLOGENETIC DATA ANALYSIS USING R #PHYL
Dr. Emmanuel Paradis – Date and location to be confirmed

Oliver Hooker PhD.
PR statistics

most recent publication - The physiological costs of prey switching 
reinforce foraging specialization - Journal of animal ecology - 
http://onlinelibrary.wiley.com/doi/10.1111/1365-2656.12632/full
prstatistics.com
facebook.com/prstatistics/
twitter.com/PRstatistics
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3/1, 128 Brunswick Street
Glasgow
G1 1TF

+44 (0) 7966500340

-- 
Oliver Hooker PhD.
PR statistics

most recent publication - The physiological costs of prey switching 
reinforce foraging specialization - Journal of animal ecology - 
http://onlinelibrary.wiley.com/doi/10.1111/1365-2656.12632/full
prstatistics.com
facebook.com/prstatistics/
twitter.com/PRstatistics
groups.google.com/d/forum/pr-statistics-post-course-forum
prstatistics.com/organiser/oliver-hooker/

3/1, 128 Brunswick Street
Glasgow
G1 1TF

+44 (0) 7966500340