BMI206: Statistical Methods

OVERVIEW – SYLLABUS – READING –  LABS – TUTORIALS – PROJECT

Free Training Courses

UC Berkeley DLab
Gladstone Workshops (also in person on campus)
The UC Berkeley Data Science 100 introductory course.

UCSF Wynton Cluster

Shared public data on the UCSF Wynton computing cluster:

/wynton/group/databases
/wynton/group/datasets

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:

Introduction to resources for using the R programming language.
RStudio is a fantastic IDE for R. Some selling points: code completion, variable explorer, graphics window, help function viewer.
Performing statistical analyses in R.
Tutorials for statistical genetics in R.
Vector memory errors

Python resources:

Google introductory course on Python
Computer Science Online Python for Programmers
Writing python like poetry

General programming tips:

LearnXinY
UCSF Library

Cytoscape resources:

Tutorials for the user interface
How to automate Cytoscape via R or Python
RCy3 paper
Presentations on how to use Cytoscape
Ten simple rules for making network figures
Published Cytoscape networks

Network/pathway enrichment tutorials:

NEArender paper
Pathway Commons

Machine-learning resources:

Tutorial on supervised learning
Machine learning in R
A machine learning primer
Pitfalls of applying machine learning in genomics.
The problem of imbalanced classes
Documentation for scikit-learn
Building autoencoders with keras tutorial
TensorFlow playground
A quick introduction
Introduction to statistical learning
Paul G. Allen School lectures
Feature engineering and vizualization
A primer on deep learning in genomics
A list of deep learning implementations for biology

RNA-seq pipeline tutorials:

kallisto alignment free method
tximport and BioC testing packages

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:

Modern Statistics for Modern Biology
Safari books(the programming books with animals on the cover; provided free through UC System). There are multiple books on R and Python, though some are too specialized for the purposes of this class.

General Programming Tips

Consider following a style guide to make your code easier to read. (R, Python)

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.