"Genetic data analysis/exploration using R" - FUNDING AVAILABLE!
PR STATISTICS ARE PLEASED TO ANNOUNCE THAT THEY HAVE SECURED SOME FUNDING TO CONTRIBUTE TOWARDS TUITION FEES AND ACCOMMODATION WITH A LIMITED NUMBER OF ‘COURSE ONLY PLACES‘ AT £240.00 (inc VAT) or ‘ALL INCLUSIVE PLACES’ AVAILABLE AT £480.00 (inc VAT).
Applications should be sent to [log in to unmask] and contain the following.
1. Full name
2. Institute name
3. PhD subject title or Post doc research questions
4. Do you hold a funded position
5. 150 words why this course would be relevant to your research or how it would help.
Application deadline is August 1st, successful applicants will be notified by the 3rd August.
Full course details are given below
Delivered by Dr. Thibaut Jombart
This course will run from 16th – 20th August, Millport Field Station, Ilse of Cumbrae, Scotland
This course will provide an extensive overview of exploratory methods for the analysis of genetic data using the R software and aim to equip participants with powerful resources for tackling increasingly common challenges in genetic data analysis.
The course is aimed at PhD students, research postgraduates, and practicing academics as well as persons in industry working with genetic data in fields such as molecular ecology, evolutionary biology, and phylogenetics. This course will provide a comprehensive introduction to various statistical approaches for the analysis of genetic data.
Course content is as follows
Day 1 Introduction to phylogenetic reconstruction
• Lecture 1a: Reconstructing phylogenies from genetic sequence data. Three main approaches covered: distance-based phylogenies; maximum parsimony; and likelihood-based approaches.
• Lecture 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 Introduction to multivariate analysis of genetic data
• Lecture 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
• Lecture 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 structure
• Lecture 4: Discussing the origin and significance of spatial genetic patterns, and how to test or 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, glmnet.
Main packages: adegenet, glmnet.
Day 5 Using R for reproducible science
• Lecture 5: Using R for reproducible science.
• Practical 5: Practical session based on morning lecture
• Main packages: knitr, Sweave, rmarkdown
• Option to discuss own data (time permitting)
Please email any inquiries to [log in to unmask] or visit our website www.prstatistics.com
Please feel free to distribute this material anywhere you feel is suitable
Upcoming courses - email for details [log in to unmask]
1. INTRODUCTION TO BIOINFORMATICS USING LINUX (August)
2. INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING (August)
3. INTRODUCTION TO PYTHON FOR BIOLOGISTS (October)
4. LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R (October)
5. APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS (October)
6. PHYLOGENETIC DATA ANALYSIS USING R (October/November)
7. SPATIAL ANALYSIS OF ECOLOGIC AL DATA USING R (November)
8. ADVANCING IN STATISTICAL MODELLING USING R (December)
9. MODEL BASED MULTIVARIATE ANALYSIS OF ECOLOGICAL DATA USING R (January)
10. NETWORK ANAYLSIS FOR ECOLOGISTS USING R (March)
11. INTRODUCTION TO GEOMETRIC MORPHOMETRICS USING R (June)
Dates still to be confirmed - email for details [log in to unmask]
• STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR USING R
• INTRODUCTION TO R AND STATISTICS FOR BIOLOGISTS
• BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS
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