Course on genetic data analysuis using R

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Course on genetic data analysuis using R

Oliver Hooker
"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 [hidden email] 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

PR statistics other courses

1. 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/

2. 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/

3. 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/

4. 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/

5. 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/

6. 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/

7. 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/

8. 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/

9. 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/

10. 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/

11. 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/

12. 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/

13. ANIMAL MOVEMENT ECOLOGY (February 2018) #ANME
19th – 23rd February 2018, Wales, Dr Luca Borger, Dr. John Fieberg

14. 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/

15. 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/

16. ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R
#MVSP
Prof. Pierre Legendre, Dr. Olivier Gauthier - Date and location to be
confirmed

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

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

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

20. PHYLOGENETIC DATA ANALYSIS USING R (TBC) #PHYL
Dr. Emmanuel Paradis – Date and location to be confirmed


--------------------------------------------------------------------------------------------------------------

PR informatics other courses

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

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

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

4. 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/

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

6. EUKARYOTIC METABARCODING
23rd – 27th July 2018, Scotland, Dr. Owen Wangensteen
http://www.prinformatics.com/course/eukaryotic-metabarcoding-eukb01/

7. CODING, DATA MANAGEMENT AND SHINY APPLICATIONS USING RSTUDIO FOR
EVOLUTIONARY BIOLOGISTS AND ECOLOGISTS #CDSR
Dr. Aline Quadros



Oliver Hooker PhD.
PR statistics

2017 publications -

Ecosystem size predicts eco-morphological variability in post-glacial
diversification. Ecology and Evolution. In press.

The physiological costs of prey switching reinforce foraging
specialization. Journal of animal ecology.

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