[R-sig-genetics] Analysing Environmental Adaptation Using Landscape Genomics in R (EDAP01)
Oliver Hooker
o||verhooker @end|ng |rom pr@t@t|@t|c@@com
Fri May 24 00:44:28 CEST 2019
Analysing Environmental Adaptation Using Landscape Genomics in R (EDAP01)
https://www.prstatistics.com/course/adaptive-landscape-genomics-in-r-edap01/
This course will be delivered by Matt Fitzpatrack and Dr Aki Laruson form
the 15th - 19th July in Glasgow City Centre.
Course Overview:
Local adaptation to climate and other environmental drivers increasingly is
being studied at the molecular level using high-throughput sequencing
methods, with applications spanning both model and non-model organisms. At
the same time, statistical tools for modeling and mapping patterns of
biodiversity have seen increasing application, including to the challenge
of understanding the drivers of spatial variation in adaptive genomic
variation and mapping these patterns under current and future climate. This
5-day course will provide the skill set necessary to analyze sequence data
for signatures of natural selection and to apply spatial modeling
techniques to these patterns to quantify and map population-level genetic
variation using two spatial modelling algorithms – Generalized
Dissimilarity Modelling (GDM) and Gradient Forest (GF).
The course will include introductory lectures, instruction on using the
Linux command line for manipulation of genomic data, guided computer coding
in R, and exercises for the participants, with an emphasis on visualization
and reproducible workflows. Portions of each day will be allotted for
students to work through their own datasets with the instructors.
Course Programme
Sunday 14th
Meet at the accommodation at approx. 17:00 onwards
Monday 15th – Classes from 09:00 to 17:00
Day 1 – Background and introduction
1) Introduction to approach
2) Data types (spatial, environmental, and genomic)
3) Considerations (quality control, SNP calling, filtering)
Tuesday 16th – Classes from 09:00 to 17:00
Day 2 – Natural Selection I
4) Introduction to the genomics of natural selection
5) Review of population genomic approaches to inferring selection
6) Implementing FST- and differentiation-outlier tests and interpreting
results
Wednesday 17th – Classes from 09:00 to 17:00
Day 3 – Natural selection II
7) Principles of inferring selection from environmental association analyses
8) Review of landscape genomics approaches to inferring selection
9) Preparing SNP data from VCF and environmental data from rasters
10) Implementing multiple association methods (e.g., LFMM, RDA, etc.) and
interpreting results
Thursday 18th – Classes from 09:00 to 17:00
Day 4 – Spatial Modeling I
11) Introduction to GDM and GF
12) Review of genetic and environmental data preparation
13) Interpreting model results
14) Model fitting / testing / validation / variable selection
Friday 19th – Classes from 09:00 to 16:30
Day 5 – Spatial Modeling II
15) Predictions & Applications of GDM / GF
16) Transforming environmental grids
17) Visualizing spatial variation in genetic composition
18) Calculating genetic differences between locations / times
19) Projecting patterns under climate change
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1. June 10th – 14th 2019
STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR (SIMM04)
Glasgow, Scotland, Dr. Andrew Parnell, Dr. Andrew Jackson
www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm04/
2. June 10th – 14th 2019
INTRODUCTION TO PYTHON FOR BIOLOGISTS (IPYB06)
Glasgow, Scotland, Dr. Martin Jones
http://www.prinformatics.com/course/introduction-to-python-for-biologists-ipyb06/
3. June 17th – 21st 2019
ADVANCED PYTHON FOR BIOLOGISTS (APYB03)
Glasgow, Scotland, Dr. Martin Jones
www.prinformatics.com/course/advanced-python-biologists-apyb03/
4. June 24th – 28th 2019
MICROBIOME DATA ANALYSIS USING QIIME2 (MBQM01)
Glasgow, Scotland, Dr. Yoshiki Vazquez Baeza, Dr. Antonio Gonzalez Pena
https://www.prinformatics.com/course/microbiome-data-analysis-using-qiime2-mbqm01/
5. July 1st – 5th 2019
BIOACOUSTICS FOR ECOLOGISTS: HARDWARE, SURVEY DESIGN AND DATA ANALYSIS
(BIAC01)
Glasgow, Scotland, Dr. Paul Howden-Leach
https://www.prstatistics.com/course/bioacoustics-for-ecologists-hardware-survey-design-and-data-analysis-biac01/
6. July 8th – 12th 2019
INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING USING R (IBHM03)
Glasgow, Scotland, Dr. Andrew Parnell
https://www.psstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm03/
7. July 15th – 19th 2019
ANALYSING ENVIRONMENTAL ADAPTATION USING LANDSCAPE GENETICS (EDAP01)
Glasgow, Dr. Matt Fitzpatrick
https://www.prstatistics.com/course/analysing-environmental-adaptation-using-landscape-genetics-edap01
8. July 29th – August 2nd 2019
INTRODUCTION TO SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R (ISPE01)
Glasgow, Scotland, Dr. Jakub Nowosad
https://www.prstatistics.com/course/introduction-to-spatial-analysis-of-ecological-data-using-r-ispe01/
9. September 2nd – 6th 2019
APPLIED METHODS FOR ANALYSING CAPTURE-RECAPTURE (MARK-RECAPTURE) DATA USING
SPATIALLY EXPLICIT AND NON-SPATIAL TECHNIQUES (MARK01)
Glasgow, Scotland, Dr. Joanne Potts, Dr. David Borchers
https://www.prstatistics.com/course/applied-methods-for-analysing-capture-recapture-mark-recapture-data-using-spatially-explicit-and-non-spatial-techniques-mark01/
10. September 9th – 13th 2019
DATA SCIENCE/ANALYTICS USING PYTHON (DSAP01)
Glasgow, Scotland, Dr. Mark Andrews
https://www.psstatistics.com/course/data-science-analytics-using-python-dsap01/
11. September 16th – 20th 2019
R PACKAGE DESIGN AND DEVELOPMENT AND REPRODUCIBLE DATA SCIENCE FOR
BIOLOGISTS (RPKG01)
Glasgow, Scotland, Dr. Cory Merow, Dr. Andy Rominger
https://www.prstatistics.com/course/r-package-design-and-development-and-reproducible-data-science-for-biologists-rpkg01/
12. September 16th – 20th 2019
STRUCTURAL EQUATION MODELLING AND PATH ANALYSIS (SMPA01)
Glasgow, Scotland, Dr. Mark Andrews
https://www.psstatistics.com/course/structural-equation-modelling-and-path-analysis-smpa01/
13. September 23rd – 27th 2019
GENERALISED LINEAR (GLM), NONLINEAR (NLGLM) AND GENERAL ADDITIVE MODELS
(GAM’S) (GNAM01)
Glasgow, Scotland, Dr. Mark Andrews
https://www.psstatistics.com/course/generalised-linear-glm-nonlinear-nlglm-and-general-additive-models-gam-gnam01/
14. September 30th – October 4th 2019
GEOMETRIC MORPHOMETRICS USING R (GMMR02)
Glasgow, Scotland, Prof. Dean Adams, Prof. Michael Collyer, Dr. Antigoni
Kaliontzopoulou
http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr02/
15. October 7th – 11th 2019
CONSERVATION PLANNING USING PRIORITIZR : FROM THEORY TO PRACTICE (PRTZ01)
Athens, GREECE, Dr Richard Schuster and Nina Morell
https://www.prstatistics.com/course/conservation-planning-using-prioritizr-from-theory-to-practice-prtz01/
16. October 14th – 18th 2019
INTRODUCTION TO BEHAVIOURAL DATA ANALYSIS USINR R (IBDA01)
Glasgow, Scotland, Dr Will Hoppitt
https://www.psstatistics.com/course/introduction-to-behavioural-data-analysis-using-r-ibda01/
17. November 4th – 8th 2019
Glasgow, Scotland, Dr. Mark Andrews
INTRODUCTION TO BAYESIAN DATA ANALYSIS FOR SOCIAL AND BEHAVIOURAL SCIENCES
USING R AND STAN (BDRS02)
https://www.psstatistics.com/course/introduction-to-bayesian-data-analysis-for-social-and-behavioural-sciences-using-r-and-stan-bdrs02/
18. November 4th – 8th 2019
BEHAVIOURAL DATA ANALYSIS USING MAXIMUM LIKELIHOOD (BDML01)
Glasgow, Scotland, Dr Will Hoppitt
https://www.psstatistics.com/course/behavioural-data-analysis-using-maximum-likelihood-bdml02/
19. November 11th – 15th 2019
APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS (ABME05)
Glasgow, Scotland, Dr Matt Denwood, Emma Howard
https://www.prstatistics.com/course/applied-bayesian-modelling-for-ecologists-and-epidemiologists-abme05/
20. November 18th – 22nd 2019
INTRODUCTION TO STRUCTURED POPULATION MODELS AND DEMOGRAPHIC DISTRIBUTION
MODELS (IIPM01)
Athens, GREECE, Dr Cory Merow
https://www.prstatistics.com/course/introduction-to-structured-population-models-and-demographic-distribution-models-iipm01/
21. November 25th – 29th 2019
ADVANCED RANGE, NICHE, AND DISTRIBUTION MODELING (ASDM01)
Athens, GREECE, Dr Cory Merow
https://www.prstatistics.com/course/advanced-range-niche-and-distributio
--
Oliver Hooker PhD.
PR statistics
2019 publications;
A way forward with eco evo devo: an extended theory of resource
polymorphism with postglacial fishes as model systems. Biological Reviews
(2019).
prstatistics.com
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