Course outside EMBL-EBI
CABANA Workshop: Genomic Analysis of Crop Biodiversity using R
This course will provide training on using R in genomics applications for crop biodiversity. The first day will cover the basics of biodiversity and R, before analyzing various genomes to assess biodiversity. This will include hierarchical clustering, correlating genomic data with geographic and phenotypic information and investigating gene-phenotype relationships and microsatellites. This course will use genomic data of wheat, maize and chilli pepper as training datasets throughout the week.
This course will be jointly taught by Octavio Martinez de la Vega (LANGEBIO, Cinvestav) and Manuel Humberto Reyes-Valdes (UAAAN).
Who is this course for?
This course is aimed at researchers from postgraduate level upwards interested in using R to analyse genomics data for crop biodiversity studies.
Please note this course will be taught in English, however the trainers are fluent in Spanish, and can offer language support where feasible.
A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form.
An undergraduate level degree in plant biology or a related discipline would be an advantage.
You will need to know basic commands in R in order to get the most from this course, though a review of basic concepts and commands in R will be covered on the first day. You can find a good introduction to R here: http://www.r-tutor.com/r-introduction
You will also need to bring a laptop with R installed and working knowledge of how to navigate your working directory effectively using R commands.
To download R please visit: https://www.r-project.org/
To download RStudio please visit: https://www.rstudio.com/products/rstudio/download/
What will I learn?
After this course you should be able to:
- Input and analyze genomic data into R to evaluate genomic diversity
- Discuss advantages and limitations of different data types
- Select the best method to analyze genomic diversity
- Draw and evaluate dendrograms showing genomic relations
- Plan genomic experiments to optimal evaluation of genomic diversity
LANGEBIO, Cinvestav, Mexico
Universidad Autónoma Agraria Antonio Narro (UAAAN), Mexico
Day 1 – Tuesday 25 June 2019
|09:00-10:00||Welcome and Introduction|
|10:00-11:00||Genomic Molecular Markers|
|11:30-13:00||R packages for biodiversity|
|14:00-15:30||Overview of R|
|16:00-17:00||Guidelines for analysis of biodiversity|
|17:00-17:30||Data simulation: Dummy examples|
|17:30||End of day 1|
Day 2 – Wednesday 26 June 2019
|10:00-11:00||Hierarchical clustering and dendrograms|
|14:00-15:30||Wheat data from CIMMYT|
|16:00-17:00||Assessing diversity in wheat data|
|17:00-17:30||Summarizing diversity in wheat data|
|17:30||End of day 2|
Day 3 – Thursday 27 June 2019
|09:00-10:00||Testing diversity in wheat data|
|10:00-11:00||Selecting for conservation in wheat data|
|14:00-15:30||Assessing diversity in maize microsatellites|
|16:00-17:00||Summarizing diversity in maize microsatellites|
|17:00-17:30||Testing diversity in maize microsatellites|
|17:30||End of day 3|
Day 4 – Friday 28 June 2019
|09:00-10:00||Selecting for conservation in maize microsatellites|
|11:30-13:00||Assessing diversity in Genome-wide Phenotypes|
|14:00-15:30||Summarizing diversity in Genome-wide Phenotypes|
|16:00-17:00||Testing diversity in Genome-wide Phenotypes|
|17:00-17:30||Design of biodiversity studies|
|17:30-17:45||Course close and feedback|
In order to be considered for a place on this course applicants must complete the online application form.
Incomplete applications will NOT be considered.
Please note that the registration fee of $700MXN includes:
- All meals (breakfast, lunch, dinner and refreshment breaks)
- Accommodation for 5 nights at Hotel IBIS Irapuato
- Course materials (Course notes in PDF, Datasets and functions in R)
- Course dinner on Thursday 27 June, 2019.
There will be a maximum of 25 participants on this course and registration is dependent on selection after successful completion of the application process.
Registration will close on 28 May 2019 at 10:00 (British Summer Time)
If you have any queries about the registration process please email Guilherme Oliveira and Piv Gopalasingam.