Microbiome Bioinformatics Analysis
General Information
Code: BIOF-Mic101
Instructor: Dr. Mona Parizadeh (Ph.D., PDF)
Organized by: ICOIA (International Community of Iranian Academics)
Start Date:
- Esfand 15, 1403 - 7 PM IRAN
Objective: Metabarcoding and 16S rRNA gene sequencing using R
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: icoia.onlineschool@gmail.com
Register: here
To ask questions about the course, communicate with the instructor and get informed about other free training courses, become a member of the ICOIA Online School Telegram Group.
Audience
This course is suitable for:
- Levels: Beginner & Intermediate
- Fields: Biology, Medicine, Veterinary, and Agriculture & Natural Resources
- Language: Farsi
This course covers the following material:
- Introduction to metabarcoding and amplicon sequencing
- Introduction to R
- DADA2 Tutorial
- 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
- Wrap up of the results of 16S rRNA gene sequence analysis
Setup
To participate in this Workshop, please install the following software, 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 TutorialLinux (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.
R for beginners
To follow the workshop, you must have a basic understanding of R. Before attending the workshop, please go through the following courses: