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DNA Variant Analysis with R Bioconductor

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 Karla Lindquist

Date:
Tuesday, June 4, 2019
Time:
2:00pm - 5:00pm
Location:
BH215
Campus:
Mission Bay
Categories:
  Bioinformatics and Statistics     Data Science Initiative     Programming  
Registration has closed.

Event Organizer

Profile photo of Karla Lindquist
Karla Lindquist