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        Sept. 2019 Microbial Community Analysis Workshop

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Introduction and Lectures
Intro to the Workshop and Core
What is Bioinformatics?
Experimental Design and Cost Estimation
Introduction to Command-Line and the Cluster
Logging in and Transferring Files
Intro to Command-Line
Advanced Command-Line (extra)
Running jobs on the Cluster and using modules
Intro to R and Rstudio
Getting Started
Intro to R
Prepare Data in R (extra)
Data in R (extra)
dbcAmplicons
dbcAmplicons Installing Software
dbcAmplicons - Amplicons talk
dbcAmplicons - Bioinformatics talk
Dataset and Metadata
dbcAmplicons - Data processing
dbcAmplicons w/Dada2
Coming soon
Microbial Community Analysis in R
Prepare MCA Analysis
MCA Analysis in phyloseq
Support
Cheat Sheets
Software and Links
Scripts
ETC
Closing thoughts
Workshop Photos
Github
Biocore website

Software and Links

Software

  1. R Project
    Install from the website

  2. RStudio
    Install from the website

  3. Apache ant needed for RDP classifier

  4. Java8, needed for RDP Classifier

  5. Python2.7, Python 2.7 is needed for this workshop

  6. FLASH2

  7. RDP classifier