UC Davis Genome Center Bioinformatics Core

Welcome

What is Bioinformatics

Introductory Command line and cluster

• Logging In and transferring files
• Intro to command-line
• Running jobs on the Cluster and using modules

Experimental Design and Cost Estimation (talk)

dbcAmplicons

• Installing Software
• dbcAmplicons: Amplicons (talk)
• dbcAmplicons: Bioinformatics (talk)
• dbcAmplicons: Data processing, 16S V1-V3
• dbcAmplicons: Data processing, other amplicons

dataset metadata

• sample submission
• barcode table
• primer table
• sample sheet

Intro to R and Rstudio

• Getting Started
• Intro to R

  EXTRA

• Prepare Data in R
• Data in R

Microbial Community Analysis in R

• MCA Analysis in phyloseq
  • phyloseq.Rmd

Closing thoughts

Cheat Sheets

Cheat Sheets