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5 | 5 |
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6 | 6 | <br> |
7 | 7 |
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8 | | -> For a guided introduction to the package, start with the **[vignette suite](#vignettes)** below. |
9 | | -> The remainder of this README contains extended worked examples and required project information. |
| 8 | +> For a guided introduction to the package, start with the **[vignette |
| 9 | +> suite](#vignettes)** below. The remainder of this README contains |
| 10 | +> extended worked examples and required project information. |
10 | 11 |
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11 | 12 | ## Contents |
12 | 13 |
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16 | 17 | - [Background](#background) |
17 | 18 | - [Why are Pfizer sharing this?](#why-are-pfizer-sharing-this) |
18 | 19 | - [What is the benefit of this work?](#what-is-the-benefit-of-this-work) |
19 | | -- [How should I submit questions, queries and enhancements?](#how-should-i-submit-questions-queries-and-enhancements) |
| 20 | +- [How should I submit questions, queries and |
| 21 | + enhancements?](#how-should-i-submit-questions-queries-and-enhancements) |
20 | 22 | - [How does Hotgenes work?](#how-does-hotgenes-work) |
21 | | -- [What can you do with a Hotgenes object?](#what-can-you-do-with-a-hotgenes-object) |
22 | | -- [All functionality is available in a shiny app!](#all-functionality-is-available-in-a-shiny-app) |
| 23 | +- [What can you do with a Hotgenes |
| 24 | + object?](#what-can-you-do-with-a-hotgenes-object) |
| 25 | +- [All functionality is available in a shiny |
| 26 | + app!](#all-functionality-is-available-in-a-shiny-app) |
23 | 27 | - [Explore functions](#explore-functions) |
24 | 28 | - [Code of Conduct](#code-of-conduct) |
25 | 29 |
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26 | 30 | ## Vignettes |
27 | 31 |
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28 | 32 | The package documentation is organized into the following vignettes: |
29 | 33 |
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30 | | -- [01 Creating Hotgenes Objects](vignettes/01_Creating_Hotgenes_Objects.md) |
| 34 | +- [01 Creating Hotgenes |
| 35 | + Objects](vignettes/01_Creating_Hotgenes_Objects.md) |
31 | 36 | - [02 API and Methods](vignettes/02_API_and_Methods.md) |
32 | | -- [03 Visualization, Exploration, and Enrichment](vignettes/03_Visualization_and_Exploration.md) |
33 | | -- [04 Using Shiny to Prioritize Genes of Interest](vignettes/04_Interactive_Exploration_Shiny.md) |
34 | | -- [05 Sample-wise Pathway Activity with HotgeneSets](vignettes/05_Samplewise_Pathway_Activity_HotgeneSets.md) |
| 37 | +- [03 Visualization, Exploration, and |
| 38 | + Enrichment](vignettes/03_Visualization_and_Exploration.md) |
| 39 | +- [04 Using Shiny to Prioritize Genes of |
| 40 | + Interest](vignettes/04_Interactive_Exploration_Shiny.md) |
| 41 | +- [05 Sample-wise Pathway Activity with |
| 42 | + HotgeneSets](vignettes/05_Samplewise_Pathway_Activity_HotgeneSets.md) |
35 | 43 |
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36 | 44 | ## Installation requires R (\>= 4.2.0); however R (\>= 4.3.0) is recommended |
37 | 45 |
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