Resources

There are many open-source resources in bioinformatics. Here, we highlight UWISDOM’s contributions as well as outside resources we’ve learned from in the past. This is not an exhaustive list by any means, and we welcome recommendations sent to uwisdom@uw.edu!

UWISDOM

  • Workshops
  • Tutorials
  • Software
    • SEAsnake for processing fastq sequences to counts data used in our workshops
    • kimma for flexible mixed effects models of omics data

Beginner coders

  • The Carpentries for Unix, R, python, git, and more!
  • BioInformatics Group at South Lake Union (BIGslu) for R and git
  • Swirl for interactive R courses
  • EDUCE at the U of British Columbia for R with a focus on microbiome data and statistics
  • Riffomonas Dr. Pat Schloss’s coding club with open-source materials and recordings
  • R cheatsheets also available in RStudio under Help > Cheatsheets

RNA-seq analysis

  • SEAsnake for processing fastq sequences to counts data used in our workshops
  • kimma for flexible mixed effects model design
  • limma for linear modeling (Chapter 15: RNA-Seq Data)
  • dream for paired sample designs

Local groups and meetups