https://github.com/icoia/microbiome_bioinformatics_analysis_2025
Metabarcoding and 16S rRNA Gene Sequencing (BIOF-Mic101)
https://github.com/icoia/microbiome_bioinformatics_analysis_2025
16s dada2 metaanalysis metabarcoding microbiome microbiome-analysis microbiome-data statistical-analysis
Last synced: 9 months ago
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Metabarcoding and 16S rRNA Gene Sequencing (BIOF-Mic101)
- Host: GitHub
- URL: https://github.com/icoia/microbiome_bioinformatics_analysis_2025
- Owner: icoia
- License: gpl-3.0
- Created: 2025-02-24T05:32:54.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-04-08T10:56:42.000Z (about 1 year ago)
- Last Synced: 2025-04-08T11:29:52.506Z (about 1 year ago)
- Topics: 16s, dada2, metaanalysis, metabarcoding, microbiome, microbiome-analysis, microbiome-data, statistical-analysis
- Language: R
- Homepage: https://icoia.github.io/microbiome_bioinformatics_analysis_2025/
- Size: 315 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 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 Tutorial
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.
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:
- Introduction to R (1)
- Introduction to R (2)
- Programming with R
Download database for taxonomic assignment with DADA2
- silva_nr99_v138.2_toGenus_trainset.fa.gz
- silva_nr99_v138.2_toSpecies_trainset.fa.gz
Download data for microbial analysis with DADA2