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4 changes: 2 additions & 2 deletions docs/404.html
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<title>Page not found | AnVIL CoFests! 2024</title>
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4 changes: 2 additions & 2 deletions docs/About.md
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## collate en_US.UTF-8
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## date 2024-10-18
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## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
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8 changes: 4 additions & 4 deletions docs/about-the-authors.html
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>About the Authors | AnVIL CoFests! 2024</title>
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<meta name="date" content="2024-10-18" />
<meta name="date" content="2024-11-07" />

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## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2024-10-18
## date 2024-11-07
## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## bookdown 0.40 2024-07-02 [1] CRAN (R 4.3.2)
## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2)
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4 changes: 2 additions & 2 deletions docs/brainstorming-feature-requests-for-anvil.html
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Chapter 4 Brainstorming Feature Requests for AnVIL | AnVIL CoFests! 2024</title>
<meta name="description" content="Description about Course/Book." />
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<meta property="og:title" content="Chapter 4 Brainstorming Feature Requests for AnVIL | AnVIL CoFests! 2024" />
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<meta name="date" content="2024-10-18" />
<meta name="date" content="2024-11-07" />

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<title>Chapter 1 Deploying, Training, and Interpreting Deep Learning Models for regulatory genomics in AnVIL | AnVIL CoFests! 2024</title>
<meta name="description" content="Description about Course/Book." />
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<meta name="date" content="2024-10-18" />
<meta name="date" content="2024-11-07" />

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4 changes: 2 additions & 2 deletions docs/how-to-run-your-tool-in-anvil-with-wdl.html
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<title>Chapter 3 How to Run Your Tool in AnVIL with WDL | AnVIL CoFests! 2024</title>
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<meta name="date" content="2024-10-18" />
<meta name="date" content="2024-11-07" />

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6 changes: 3 additions & 3 deletions docs/index.html
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>AnVIL CoFests! 2024</title>
<meta name="description" content="Description about Course/Book." />
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<meta name="date" content="2024-10-18" />
<meta name="date" content="2024-11-07" />

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</div>
<div id="header">
<h1 class="title">AnVIL CoFests! 2024</h1>
<p class="date"><em>October 18, 2024</em></p>
<p class="date"><em>November 07, 2024</em></p>
</div>
<div id="what-are-cofests" class="section level1 unnumbered hasAnchor">
<h1>What are CoFests!?<a href="index.html#what-are-cofests" class="anchor-section" aria-label="Anchor link to header"></a></h1>
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---
title: "AnVIL CoFests! 2024"
date: "October 18, 2024"
date: "November 07, 2024"
site: bookdown::bookdown_site
documentclass: book
bibliography: book.bib
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<title>Organizer Guide | AnVIL CoFests! 2024</title>
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<meta name="date" content="2024-10-18" />
<meta name="date" content="2024-11-07" />

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7 changes: 5 additions & 2 deletions docs/polygenic-risk-score-prs-analysis-in-anvil.html
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<title>Chapter 2 Polygenic Risk Score (PRS) Analysis in AnVIL | AnVIL CoFests! 2024</title>
<meta name="description" content="Description about Course/Book." />
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<meta name="date" content="2024-10-18" />
<meta name="date" content="2024-11-07" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
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<h1><span class="header-section-number">Chapter 2</span> Polygenic Risk Score (PRS) Analysis in AnVIL<a href="polygenic-risk-score-prs-analysis-in-anvil.html#polygenic-risk-score-prs-analysis-in-anvil" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<p>Led by: Matthew Lebo, Harvard Medical School</p>
<p>AnVIL Outreach coordinator: Elizabeth Humphries</p>
<p>About This Track</p>
<p>This track, run by the AnVIL Clinical Resource team, will consist of both an overview and a hands-on workshop to provide individuals with an understanding of polygenic scores and how to run and evaluate them in AnVIL. First, we will level-set by providing an overview of the current state of polygenic analysis, with a focus on polygenic risk scores (PRS). Next, we will jointly work with participants to run PRS analyses in AnVIL using the WDL framework. These tasks will increase in complexity in terms of analytical components of the workflow, with the goal of enabling users to run the WDL on their own. We will also engage with participants to get feedback and create user-friendly documents to enable processing of this workflow once published to the broader community. Finally, we will work with more advanced users to generate a new WDL focused on the evaluation of PRS among a cohort of individuals.</p>
<p>Participants are not required to supply their own data, as publicly available data and an AnVIL workspace will be provided as part of the CoFest track. Users who are interested in running the analyses on their own data are welcome, but should have their own workspace in which to run the analyses.</p>

</div>
<hr>
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Led by: Matthew Lebo, Harvard Medical School

AnVIL Outreach coordinator: Elizabeth Humphries

About This Track



This track, run by the AnVIL Clinical Resource team, will consist of both an overview and a hands-on workshop to provide individuals with an understanding of polygenic scores and how to run and evaluate them in AnVIL. First, we will level-set by providing an overview of the current state of polygenic analysis, with a focus on polygenic risk scores (PRS). Next, we will jointly work with participants to run PRS analyses in AnVIL using the WDL framework. These tasks will increase in complexity in terms of analytical components of the workflow, with the goal of enabling users to run the WDL on their own. We will also engage with participants to get feedback and create user-friendly documents to enable processing of this workflow once published to the broader community. Finally, we will work with more advanced users to generate a new WDL focused on the evaluation of PRS among a cohort of individuals.



Participants are not required to supply their own data, as publicly available data and an AnVIL workspace will be provided as part of the CoFest track. Users who are interested in running the analyses on their own data are welcome, but should have their own workspace in which to run the analyses.
4 changes: 2 additions & 2 deletions docs/references.html
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<title>Chapter 5 References | AnVIL CoFests! 2024</title>
<meta name="description" content="Description about Course/Book." />
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<meta name="date" content="2024-10-18" />
<meta name="date" content="2024-11-07" />

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