BMI206: Statistical Methods


Free Training Courses

UCSF Wynton Cluster

  • Shared public data on the UCSF Wynton computing cluster:
  • If you do not already have access to the Wynton cluster, access can be arranged for students in this class. Contact Dr. Pollard to get an account.
  • Online Resources

    These tutorials and other websites may help you to configure your laptop for the activities in the course and to brush up your programming and data analytical skills.

  • R resources:
  • Python resources:
  • General programming tips:
  • Cytoscape resources:
  • Network/pathway enrichment tutorials:
  • Machine-learning resources:
  • RNA-seq pipeline tutorials:
  • ChIP-seq pipeline tutorials:
      BioC epigenomics course
  • Package for visualization of embeddings of high-dimensional data, such as single-cell genomics.
  • Tutorial on hierarchical random effects models.
  • Books

    These books are available free online:

    General Programming Tips

  • Consider following a style guide to make your code easier to read. (RPython)
  • If you don’t already have it, Homebrew is a great utility for installing/updating applications in OSX. To install it just follow the instructions on the linked page. It does require XCode’s Command Line Tools, which you can get either as a standalone or by installing all of XCode, both of which can be downloaded from the Apple developers site. Once you have Homebrew, installing code like R, or Git, or Mercurial becomes as easy as typing “brew install _program name_” on the command line.
  • Jupyter notebooks are good for writing up projects with code.
  • If you are using Windows, you might consider installing Cygwin to get some Unix functionality, or running a Linux virtual machine.