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DNA Variant Analysis with R Bioconductor (2-part Series) Online
Overview
In this workshop, we will use R to analyze DNA variants from Variant Call Format files to identify those likely to have a functional impact. It is intended for those with intermediate R programming skills. This is a 2-part hands-on workshop series that will take place virtually in two Zoom sessions.
Objectives
- Examine the header and metadata of a Variant Call Format (VCF) file
- Select variants in genes of interest
- Get transcripts and genotypes for selected variants
- Locate regions of genes where variants fall (exons, introns, etc.)
- Get the predicted impact of variants
- Export variants to a Browser Extensible Data (BED) file and view in UCSC browser
- Perform pathway analysis on variants of interest
Prerequisites
You must have some R programming experience and a basic understanding of the purpose of DNA-Seq analysis to benefit from this course. Feel free to contact the instructor (see below) if you have questions about these requirements.
Software
Please have the latest versions of R and R Bioconductor installed on your laptop prior to the workshop. RStudio (the free version) is highly recommended as well, since we will be teaching in this environment.
Materials
Workshop materials are available online here.
Instructor
Karla Lindquist, PhD, is the Scientific Lead for the UCSF Library's Data Science Initiative.
School of Medicine's Zoom Guide for Participants.
- Dates & Times:
- 11:00am - 1:00pm, Thursday, Aug 18 2022
11:00am - 1:00pm, Friday, Aug 19 2022
- Time Zone:
- Pacific Time - US & Canada (change)
- Online:
- This is an online event. Event URL will be sent via registration email.
- Categories:
- Data Science > Bioinformatics and Statistics Data Science > Programming Data Science
