## 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

- /wynton/group/databases

/wynton/group/datasets

# 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.

- 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

- Google introductory course on Python

Computer Science Online Python for Programmers

Writing python like poetry

- 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

- NEArender paper

Pathway Commons

- 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

- BioC epigenomics course

# 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.