CABANA Workshop: Introduction to R and Bioconductor for genomic analyses

Date:

 Tuesday 21 Friday 24 May 2019

Venue: 

LANGEBIO, Cinvestav - LANGEBIO, Cinvestav, Libramiento Norte Carretera Leon Km 9.6, Irapuato,  GUA,  36821, Mexico

Application opens: 

Thursday 11 April 2019

Application deadline: 

Tuesday 30 April 2019

Participation: 

Open application with selection

Contact: 

Derrin Crawte

Registration fee: 

$700 MXN

Registration closed

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Course Overview

Bioinformatics is fast becoming an integral component of all biological projects. The deluge of genomic information has also opened up the possibility of asking new questions using only publicly available data and a personal computer. This course will go beyond bioinformatic tools that run on web interfaces. Instead, you will learn to program using R, one of the most popular languages for performing bioinformatic and statistical analyses. 

The course will begin by introducing basic R commands and scripts, and move onto the use of R in genomics. Bioconductor will be covered in the second half of the course, with the final day focussing on genome annotation and downloading data using biomaRt. 
 

Audience

The course is suitable for graduate students and young researchers with a background in biology who are keen to become proficient bioinformaticians within the fields of genomics and/or transcriptomics. We will start with the basics, so students with no prior programming knowledge are welcome. We have a number of Linux computers that you can use, and you can bring your own laptops*. 

Please note this course will be taught in English, however the trainers are fluent in either Spanish or Portuguese, 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.

*If you bring your own laptop (any operating system is fine), you must have installed the following programs: R (at least version 3.5), the latest Rstudio and Bioconductor. 

To download R please visit: https://www.r-project.org/

To download RStudio please visit: https://www.rstudio.com/products/rstudio/download/

Bioconductor must be downloaded and installed via R, instructions on how to do this can be found here: https://www.bioconductor.org/install/

Modules

  • introduction-ensemblensembl-genomes

Learning outcomes

After this course you should be able to:

  • Use R for numerical calculations and exploring data
  • Write your own programs in R
  • Use Bioconductor packages to help with your own bioinformatic problems
  • Access genome information stored in Ensembl and other databases
  • Explore genome annotation of your favourite species

Programme

Day 1: Basics of R and script writing
Day 2: Genome browsing, comparative genomics and R markdown
Day 3: Bioconductor and visualizing gene expression
Day 4: GenomicRanges and biomaRt

 

Day 1 – Tuesday 21 May 2019 - Basics of R and script writing
09:00-09:20 Welcome and registration Cei Abreu
09:20-11:00 R basics using the console (mathematical operations, saving results to objects, functions, dealing with numbers and text) Cei Abreu
11:00-11:30 Break
11:30-13:00 More R basics (relational operations, subsetting objects, reading data from files, basic plotting) Cei Abreu
13:00-14:00 Lunch
14:00-15:45 R objects and classes (data.frame, matrix, list, converting, subsetting) Benilton Carvalho
15:45-16:15 Break
16:15-18:00 Writing R scripts and automating tasks with cycles (for, apply, lapply, sapply) Benilton Carvalho
18:00 End of day 1  
Day 2 – Wednesday 22 May 2019 - Genome browsing, comparative genomics and R markdown
09:00-10:45 Ensembl genome browser (webinar) Erin Haskell
10:45-11:15 Break
11:15-13:00 Exploring and comparing genes and genomes Cei Abreu
13:00-14:00 Lunch
14:00-15:45 Reproducible programming and rich reports (R markdown) Benilton Carvalho
15:45-16:15 Break
16:15-18:00 Integration of covered material Cei Abreu / Benilton Carvalho
18:00-20:00 Social event (Faculty club)
Day 3 – Thursday 23 May 2019 - Bioconductor and visualizing gene expression
09:00-10:45 Introduction to Bioconductor (Biostrings) Cei Abreu
10:45-11:15 Break
11:15-13:00 Designing a basic motif discovery tool Cei Abreu
13:00-14:00 Lunch
14:00-15:45 Bioconductor packages for working with gene expression data Benilton Carvalho
15:45-16:15 Break
15:45-18:00 Exploring and visualizing gene expression Benilton Carvalho
18:00 End of day 3
Day 4 – Friday 24 May 2019 - GenomicRanges and biomaRt
10:00-11:00 Keynote lecture Benilton Carvalho
11:00-11:30 Break  
11:30-13:30 Exploring genome annotation with GenomicRanges Cei Abreu
13:30-14:30 Lunch
14:30-16:15 Using biomaRt to access data from Ensembl Cei Abreu
16:15-17:00 Course wrap-up and feedback Cei Abreu / Benilton Carvalho
17:00 End of course