BioData.pt Crash Course: Microbiome Visualization with Biome-Shiny
BioData.pt Crash Course: Microbiome Visualization with Biome-Shiny is an introductory one-day workshop seeking to provide users with the knowledge to create, analyze and visualize microbiome data.
The course consists of two parts: the first part, is an introduction to, and hands-on demonstration of, the DADA2 pipeline, which will be used to process a training dataset into a file that can be analyzed through the Biome-Shiny tool; the second part, employs the Biome-Shiny GUI to explore the obtained dataset's microbial community composition, as well as the alpha- and beta-diversity of the dataset, and download their results for later use.
By the end of this course, participants should be able to apply the DADA2 pipeline to process their own sequenced reads, as well as to explore their data and produce a final report using Biome-Shiny.
If you're a microbial biologist who wants to learn how to analyze microbiome data, this course is for you! Join us on the 31st of January, at the IGC!
Attending the course requires registration.
Attendance fees: The attendance fee for the course is 40€ for attending this course, or 70€ for attending both this course and the "Differential gene expression analysis in single-cell RNAseq" course, to be realized on January 30th. Attendance fees are waived for members of the BioData.pt and IGC communities.
Target audience: PhD students and post-docs who want to learn the basics of microbiome analysis in Bioinformatics, and have little knowledge of programming.
Pre-requisites: Some basic knowledge of R will be helpful, but is not necessary.
Trainers: Henrique Costa (BioData.pt/IGC), António Sousa (UBI-IGC)
Computers will be provided for participants. If you'd like, you can bring your own device, and at the end of the course we will attempt to set up the required software so you can reproduce it at home.
Morning period: 9:30-12:30 | Coffee break 10:30-11:00
- Hands-on DADA2 pipeline with a training dataset
- Assess dataset accuracy and contamination with a mock community
- Convert the ASV table with taxonomy to biom format
Afternoon period: 14:00-17:30 | Coffee break 15:45-16:15
- Introduction to Biome-Shiny: A Shiny R app for microbiome visualization
- Hands-on Biome-Shiny demonstration with the biom file
- Data filtering
- Exploring core microbiota and community composition
- Visualizing alpha- and beta-diversity
Bioinformatics Unit - IGC (UBI-IGC)
Genomics Unit - IGC (UG-IGC)