Advanced R: Variant Analysis (Fall 2020)

High Performance Computing in Biology at UIUC

HPCBio

This workshop will walk one through analyzing variant calls (VCF files) with a variety of Bioconductor packages.

Tickets are currently sold out but please add yourself to our waitlist. We often open up a few more spots, and will let you know as soon as possible if you've been added. Additionally, the waitlist gives us an idea of how much need there is for a particular workshop, and we may then choose to offer it again sooner rather than later.

<h2>Workshop Description</h2>With the support of the OVCR, HPCBio will teach a 2-part workshop, held on December 2nd &amp; 4th from 1-3pm each day. Attendees will learn how to read, filter, and interrogate variant calls that are in VCF (Variant Call Format) format with Bioconductor packages in R. Analyses may include some or all of the following topics: assessing minor allele frequency, missing data rate, heterozygosity, and/or linkage disequilibrium; working with genome annotations as TxDb objects; discovering what genes are near SNPs of interest; identifying functional consequences of variants.This workshop is appropriate for all graduate students, post-docs, and researchers. Knowledge of R programming is required! We will utilize all of these skills in this workshop. Please do not show up without these skills or you will slow the workshop down, which is unfair to the other attendees. See FAQ for alternative ways to satisfy these pre-requisites.NOTE: IF YOU PAY WITH A GRANT ACCOUNT NUMBER (THOSE STARTING WITH 1-4 AND 1-5), YOU ARE NOT GUARANTEED A SPOT IN THE WORKSHOP AND YOUR REGISTRATION WILL GET CANCELED. PLEASE SEE C-FOPAL FAQ BELOW FOR MORE DETAILS.<h2></h2><h2>FAQs</h2>What are the pre-requisites for the 10X RNA-Seq workshop?You will need to have a basic understanding and skill in R programming and a familiarity with Bioconductor. To fulfill these pre-requisites you can do one of the followingOption A : Prior knowledge<ul><li>You&#x27;ve already taken an Introduction to R &amp; Bioconductor  workshop or similar workshop.</li><li>You feel confident using R and Bioconductor that you learned on your own and/or via class work</li></ul>Option B: Self-learning<ul><li>To learn these skills independently, email us for our self-guided learning materials. </li><li>Please plan accordingly and allow at least 3-6 hours to study all the pre-requisites ahead of time.</li></ul>What are the dates and times of this workshop?The workshop will be held Dec. 2nd (Wednesday) and Dec. 4th (Friday) from 1-3pm. How do I pay using a C-FOPAL account number?Please register as a &quot;Participant (Pay $20 via UIUC account)&quot;. During checkout, please provide us with the account number you wish to use for payment. Please note that we are not able to accept grant accounts (those starting with 1-4 and 1-5). If you want to use a grant account, we suggest paying by card and then providing the receipt to your department&#x27;s business office for reimbursement.What if I need to miss a day of the workshop?All of the sessions will be recorded (assuming no technical difficulties arise), and necessary materials and slides will be posted on a workshop webpage. When do ticket sales end?We will stop selling tickets on December 1st at 5pm or when we&#x27;ve reached maximum capacity.Can you explain the workshop cost?Thanks to the generosity of the OVCR (Office of the Vice Chancellor for Research) we are able to offer our workshops for a nominal fee. Without this support, the true cost to run such workshops could be hundreds to over a thousand dollars per attendee.How can I contact the organizer with any questions?You may email us at hpcbiotraining@igb.illinois.edu for any questions pertaining to training.

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Registrations are closed

Advanced R: Variant Analysis (Fall 2020)

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Registrations are closed

Advanced R: Variant Analysis (Fall 2020)

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