DNA Variant Analysis with R Bioconductor
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.
- 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
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.
Please have the latest versions of R and R Bioconductor installed, as well as RStudio, installed on your laptop prior to the workshop.
Karla Lindquist, PhD is the Scientific Lead of the UCSF Library Data Science Initiative.
Related LibGuide: Bioinformatics and Statistics Resources by Karla Lindquist
- Tuesday, June 4, 2019
- 2:00pm - 5:00pm
- Mission Bay