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1 | 1 |
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2 | 2 | - Juicebox
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3 |
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4 | 3 | * [Introduction and Quick Start](Juicebox.wiki/Home)
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5 | 4 | * [Download](Juicebox.wiki/Download)
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6 | 5 | * [Juicebox Tutorial](Juicebox.wiki/Visualization)
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11 | 10 | * [Bookmarks](Juicebox.wiki/Bookmarks)
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12 | 11 | * [Juicebox Assembly Tools](Juicebox.wiki/Juicebox-Assembly-Tools)
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13 | 12 | * [Submapping](Juicebox.wiki/Submapping)
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14 |
| - # General |
15 | 13 | * [Compile or Contribute](Juicebox.wiki/Compile-or-Contribute)
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16 | 14 | * [Citing Juicebox](Juicebox.wiki/Citing-Juicebox)
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17 | 15 | * [FAQ](Juicebox.wiki/FAQ)
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18 |
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19 |
| - - [About Juicebox](Juicer.md) |
20 |
| - - [Understanding Hic Files](HiCFormatV8.md) |
21 |
| - - [Installing Juicebox](internalREADME.md) |
22 |
| - - [Juicebox Code of Conduct](CODE_OF_CONDUCT.md) |
23 |
| - - [Juicebox Contributors](CONTRIBUTING.md) |
| 16 | + * [About Juicebox](Juicer.md) |
| 17 | + * [Understanding Hic Files](HiCFormatV8.md) |
| 18 | + * [Installing Juicebox](internalREADME.md) |
| 19 | + * [Juicebox Code of Conduct](CODE_OF_CONDUCT.md) |
| 20 | + * [Juicebox Contributors](CONTRIBUTING.md) |
24 | 21 |
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25 | 22 | - Juicer
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26 |
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27 |
| - # Juicer |
28 | 23 | * [Introduction](juicer.wiki/Home)
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29 | 24 | * [Quick Start](https://github.com/theaidenlab/juicer/wiki/Installation#quick-start)
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30 | 25 | * [Installation](juicer.wiki/Installation)
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33 | 28 | * [Juicer in the cloud](juicer.wiki/Running-Juicer-on-Amazon-Web-Services)
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34 | 29 | * [Diploid](juicer.wiki/Diploid)
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35 | 30 | * [Data file formats](juicer.wiki/Data)
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36 |
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37 |
| - # Juicer tools |
38 | 31 | * [Download](juicer.wiki/Download)
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39 | 32 | * [Quick Start](juicer.wiki/Juicer-Tools-Quick-Start)
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40 | 33 | * [`.hic` File Creation with Pre](juicer.wiki/Pre)
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50 | 43 | * [Pearsons](juicer.wiki/Pearsons)
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51 | 44 | * [Eigenvector](juicer.wiki/Eigenvector)
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52 | 45 | * [Compare Lists](juicer.wiki/Compare-Lists)
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53 |
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54 |
| - # General |
55 | 46 | * [FAQs](juicer.wiki/FAQs)
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56 | 47 | * [Citing Juicer](juicer.wiki/Citing-Juicer)
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57 | 48 |
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58 |
| - - [Getting started with Juicer](juicer_README.md) |
59 |
| - - [Juicer Code of Conduct](juicer_CODE_OF_CONDUCT.md) |
60 |
| - - [Juicer Contributors](juicer_CONTRIBUTING.md) |
| 49 | + * [Getting started with Juicer](juicer_README.md) |
| 50 | + * [Juicer Code of Conduct](juicer_CODE_OF_CONDUCT.md) |
| 51 | + * [Juicer Contributors](juicer_CONTRIBUTING.md) |
61 | 52 |
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62 | 53 | - Straw
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63 | 54 | * [Straw Home](straw.wiki/Home.md)
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64 | 55 | * [C++](straw.wiki/CPP.md)
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65 | 56 | * [Download](straw.wiki/Download.md)
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66 | 57 | * [Python](straw.wiki/Python.md)
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67 | 58 | * [R](straw.wiki/R.md)
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68 |
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69 |
| - - [Getting started with Straw](straw_README.md) |
70 |
| - - [Straw Contributors](straw_CONTRIBUTING.md) |
71 |
| - - [Straw Code of Conduct](straw_CODE_OF_CONDUCT.md) |
72 |
| - - [Using Straw in Python](pybind11_README.md) |
| 59 | + * [Getting started with Straw](straw_README.md) |
| 60 | + * [Straw Contributors](straw_CONTRIBUTING.md) |
| 61 | + * [Straw Code of Conduct](straw_CODE_OF_CONDUCT.md) |
| 62 | + * [Using Straw in Python](pybind11_README.md) |
73 | 63 |
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74 | 64 | - [About Us](README.md)
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75 | 65 | - [Contact](something.md)
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