The goal of this course is to teach students how to gain and communicate insights from biomedical data. We will learn concepts such as data wrangling, exploratory data analysis, statistical inference, and linear and mixed modelling techniques. Students will learn to use the statistical programming language R (free and open source) throughout the complete research pipeline: importing, wrangling, visualizing, analyzing, interpreting, communicating, and collaborating. We will also learn to create and maintain efficient workflows for reproducible research. We will use modern teaching materials including DataCamp.com to introduce and reinforce R skills in an interactive self-guided environment, and the free online textbooks “Modern Dive” (Ismay & Kim, 2018) and “Data Analysis for Life Sciences” (Izarry & Love, 2015).
The course is organized into 5 blocks: working with data (3 weeks), linear models (3 weeks), inference (3 weeks), mixed models (1.5 weeks), and communication (1.5. weeks). Each class will be a mixture of didactic lectures (≈20 minutes), followed by hands-on labs to apply knowledge to real-world data. Pre-work will involve relevant readings and sometimes coding assignments to prepare for labs. For students who already have facility with R, more advanced stretch exercises will be provided. Each block will wrap up with an in-depth lab to allow students to integrate and iterate on knowledge gained, and review and relate back to previously learnt concepts. Final projects will be described in the first week of class.
Select lab sessions will require a finished submitted in-class and/or accompanying homework assignment (due via electronic submission prior to the next meeting time). Each participant must also present during the final two weeks of class. A portion of the grade will reflect attendance. Final grading rubric will be made available at the start of class.
We will be assigning some DataCamp courses/chapters to help you learn R alongside data science and analysis skills. I will enroll you in our course group on the DataCamp site using your OHSU email address, unless you provided a different email account in our pre-course survey. You will then receive an email from DataCamp with a link to register on their site. You may register with your OHSU username, but you do not have to- you may pick a different username. Please note:
Laptops will be used during the hands-on, in-class labs. If you do not have access to a laptop, please consult with the course director to make arrangements to borrow a laptop with the necessary software installed.
Attendance and class participation are expected of all students. Requests for time off must be submitted to the course director in a timely manner.
OHSU is committed to inclusive and accessible learning environments in compliance with federal and state law. If you have a disability or think you may have a disability (mental health, attention-related, learning, vision, hearing, physical or health impacts) contact the Office for Student Access at (503) 494-0082 or studentaccess@ohsu.edu to have a confidential conversation about academic accommodations. Information is also available at www.ohsu.edu/student-access. Because accommodations may take time to implement and cannot be applied retroactively, it is important to have this discussion as soon as possible.
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