June 7, 2018
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You will need your own laptop to participate in the hands-on portion of the workshop. While there will be some power distribution throuhgout the classroom, we recommend you fully charge your computer before arrival
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You do not need to insall anything prior to the Workshop. The course will be run through RStduio Cloud which runs through a web browser on all operating systems (Windows, MacOS, Linux)
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Since the hands-on portion will run through a web browser we recommend you connect to the free conference WiFi provided by ASM prior to arriving to the course
The ASM Workshop on *"Microbiome Analysis Using R" is intended to provide an overview of the basic principles underlying microbiome analysis. While the focus will be on the practical aspects of using R to complete this analysis, discussion on best practices, study design and ecological analysis will be discussed.
A significant component of the Workshop will revolve around a simple case-study which examines the time-series response of enteric bacterial communities to several different antibiotic treatments.
An overview of the analysis steps implemented:
- Environment initiation
- Read in your data and select samples for analysis
- Variable examination and modification
- Data summary and assessment
- Taxon prevalence estimations and filtering
- Data transformation
- Subsetting
- Community composition plotting
- Alpha diversity analysis
- Beta diversity analysis
- Differential abundance testing
The data originate from a study on the bacterial microbiome of mice treated with or without antibiotics to test the affects of the microbiome on flavivirus infection (https://www.ncbi.nlm.nih.gov/PubMed/29590614).
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8:00 - 8:15: Course Intro and Installation
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8:15 - 8:30: Introduction to R and RStudio
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8:30 - 9:30: ggplot2
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9:30 - 10:00: R details and working with tables
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10:00 - 11:00: Introduction to Phyloseq
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11:00 - 12:00: Introduction to the Workshop Case Study: Antibiotic Treated Mice
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12:00 - 1:00: Lunch Break
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1:00 - 3:00: Working through the Case Study in R
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3:00 - 4:00: Wrap-up and Additional Examples and Discussion