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DNA Variant Analysis with R Bioconductor In-Person
Workshop 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.
Learning 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 to benefit from this course. Please feel free to contact the instructor if you have questions about this.
Software
Please have the latest versions of R and R Bioconductor installed, as well as RStudio, installed on your laptop prior to the workshop.
Instructor
Karla Lindquist, PhD is the Scientific Lead of the UCSF Library Data Science Initiative.
Related LibGuide: Bioinformatics and Statistics Resources by Ariel Deardorff
- Date:
- Tuesday, Jun 4 2019
- Time:
- 2:00pm - 5:00pm
- Time Zone:
- Pacific Time - US & Canada (change)
- Location:
- BH215
- Campus:
- Mission Bay
- Categories:
- Data Science > Bioinformatics and Statistics Data Science Data Science > Programming
