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DNA Variant Analysis with R Bioconductor (4-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 4-part hands-on workshop series that will take place virtually using Zoom.

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.

Related LibGuide: Bioinformatics and Statistics Resources by Karla Lindquist

Dates & Times:
9:00am - 10:00am, Monday, Dec 14 2020
9:00am - 10:00am, Wednesday, Dec 16 2020
9:00am - 10:00am, Monday, Dec 21 2020
9:00am - 10:00am, Wednesday, Dec 23 2020
Time Zone:
Pacific Time - US & Canada (change)
Campus:
Online
Categories:
  Data Science Initiative > Bioinformatics and Statistics     Data Science Initiative > Programming     Data Science Initiative  
Online:
This is an online event. Event URL will be sent via registration email.

Registration is required. There are 0 seats available.

Event Organizer

Profile photo of Karla Lindquist
Karla Lindquist