Microbiome Bioinformatics Analysis Workshop
General Information
Led by: ArrietaLab
Location: Oswaldo Cruz Foundation - Rio de Janeiro, Brazil
Dates: 3-5 April 2023
Objective: Analyzing microbial DNA sequences
Requirements:
- Laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) with administrative privileges
- Access to Wifi
- R and Rstudio installed (instructions below)
- Excel or any text editor installed (e.g. TextWrangler, Notepad, BBEdit, etc.)
Contact: mona.parizadeh@ucalgary.ca
Schedule
This workshop covers the following material:
Day 1
(9 a.m. to 12 p.m. & 1 p.m. to 4 p.m.)
- Introduction to metabarcoding and amplicon sequencing
- Introduction to R
- DADA2 Tutorial
Day 2
(9 a.m. to 12 p.m. & 1 p.m. to 4 p.m.)
- Introduction to phyloseq package in R
- Data exploration
- Statistical analyses of 16S rRNA gene sequences:
- Taxonomic composition
- Alpha diversity
- Beta diversity (ordination)
- PERmutational Multivariate ANalysis Of VAriance (PERMANOVA)
- Differential analysis
- Discussion
Setup
To participate in this Workshop, please install the following software and packages, complete the R courses for beginners, and let us know if you need any help before attending.
Install R and RStudio
R is a free and open-source programming language that is particularly powerful for data exploration, visualization, and statistical analysis. We use RStudio to interact with R.
Windows
Please download R for Windows from CRAN to install R, and also install the RStudio IDE. If you have separate user and admin accounts, please run the installers as an administrator by right-clicking on the .exe file and selecting "Run as administrator" instead of double-clicking. Otherwise, problems may arise later when installing R packages.
Video Tutorial
Mac OS X
Please download R for macOS from CRAN to install R, and also install the RStudio IDE.
Video Tutorial </p></div>
Linux (Debian, Fedora/Redhat, Ubuntu)
Please download the binary files for your distribution from
CRAN to install R, or use a package manager
(e.g. run sudo apt-get install r-base
for Debian/Ubuntu and run
sudo yum install R
for Fedora/Redhat). Additionally, please install the
RStudio IDE.