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README.md

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> For a guided introduction to the package, start with the **[vignette suite](#vignettes)** below.
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> The remainder of this README contains extended worked examples and required project information.
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> For a guided introduction to the package, start with the **[vignette
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> suite](#vignettes)** below. The remainder of this README contains
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> extended worked examples and required project information.
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## Contents
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- [Background](#background)
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- [Why are Pfizer sharing this?](#why-are-pfizer-sharing-this)
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- [What is the benefit of this work?](#what-is-the-benefit-of-this-work)
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- [How should I submit questions, queries and enhancements?](#how-should-i-submit-questions-queries-and-enhancements)
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- [How should I submit questions, queries and
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enhancements?](#how-should-i-submit-questions-queries-and-enhancements)
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- [How does Hotgenes work?](#how-does-hotgenes-work)
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- [What can you do with a Hotgenes object?](#what-can-you-do-with-a-hotgenes-object)
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- [All functionality is available in a shiny app!](#all-functionality-is-available-in-a-shiny-app)
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- [What can you do with a Hotgenes
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object?](#what-can-you-do-with-a-hotgenes-object)
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- [All functionality is available in a shiny
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app!](#all-functionality-is-available-in-a-shiny-app)
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- [Explore functions](#explore-functions)
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- [Code of Conduct](#code-of-conduct)
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## Vignettes
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The package documentation is organized into the following vignettes:
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- [01 Creating Hotgenes Objects](vignettes/01_Creating_Hotgenes_Objects.md)
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- [01 Creating Hotgenes
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Objects](vignettes/01_Creating_Hotgenes_Objects.md)
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- [02 API and Methods](vignettes/02_API_and_Methods.md)
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- [03 Visualization, Exploration, and Enrichment](vignettes/03_Visualization_and_Exploration.md)
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- [04 Using Shiny to Prioritize Genes of Interest](vignettes/04_Interactive_Exploration_Shiny.md)
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- [05 Sample-wise Pathway Activity with HotgeneSets](vignettes/05_Samplewise_Pathway_Activity_HotgeneSets.md)
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- [03 Visualization, Exploration, and
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Enrichment](vignettes/03_Visualization_and_Exploration.md)
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- [04 Using Shiny to Prioritize Genes of
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Interest](vignettes/04_Interactive_Exploration_Shiny.md)
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- [05 Sample-wise Pathway Activity with
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HotgeneSets](vignettes/05_Samplewise_Pathway_Activity_HotgeneSets.md)
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## Installation requires R (\>= 4.2.0); however R (\>= 4.3.0) is recommended
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