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Topic/compatibility data check #5314

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44dd9e3
Add tool compatibility check to PCA page
ryan-preble Feb 5, 2025
fdf49ad
Moving code from pca.js to mason page
ryan-preble Feb 7, 2025
10533f3
Move functions to separate file in js/source/entries. Add compatibili…
ryan-preble Feb 7, 2025
9dfa122
Adding tool compatibility glyphs to gwas, stability, heritability pages
ryan-preble Feb 10, 2025
0b3dd70
Fixed issue with PCA not running
ryan-preble Feb 13, 2025
afdea0f
Change dataset creation to run tool compatibility in background
ryan-preble Feb 18, 2025
49be3f0
Fixing criteria for heritability so there must be shared accessions a…
ryan-preble Feb 19, 2025
56e3f05
Shift some compatibility displays to server-side instead of AJAX
ryan-preble Feb 21, 2025
9c2d5b6
Fix compatibility column showing up on all pages
ryan-preble Feb 21, 2025
858d02f
Refactor tool compatibility on other tools to get compatibility in CX…
ryan-preble Feb 21, 2025
7da9035
Fix broken tests
ryan-preble Feb 21, 2025
8a95c9f
Adding tool compatibility page to the manual
ryan-preble Feb 21, 2025
041dadd
Trying to update docs
ryan-preble Feb 24, 2025
63919a0
update bookdown docs
invalid-email-address Feb 24, 2025
69e6c7b
Remove limits for types of input data for clustering and pca
ryan-preble Feb 25, 2025
3dbbb98
update bookdown docs
invalid-email-address Feb 25, 2025
819bb85
appeasing the linter :(
ryan-preble Feb 25, 2025
6544973
update bookdown docs
invalid-email-address Feb 25, 2025
a236d02
Trying to fix some linting issues
ryan-preble Feb 25, 2025
d91fb49
update bookdown docs
invalid-email-address Feb 25, 2025
1c7b867
Removing previous commit and adding htmlhintrc
ryan-preble Feb 25, 2025
3ad92c1
update bookdown docs
invalid-email-address Feb 25, 2025
bc69d75
Change linting rules to use .htmlhintrc
ryan-preble Feb 25, 2025
1be2b3a
update bookdown docs
invalid-email-address Feb 25, 2025
b194ec2
put .htmlhintrc in linters folder
ryan-preble Feb 25, 2025
e583a2c
Remove bad action from linter.yml
ryan-preble Feb 25, 2025
ba7097e
update bookdown docs
invalid-email-address Feb 25, 2025
18bba12
Try to make linter use .htmlhintrc
ryan-preble Feb 25, 2025
e25817c
update bookdown docs
invalid-email-address Feb 25, 2025
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5 changes: 5 additions & 0 deletions .github/linters/.htmlhintrc
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{
"head-script-disabled": false,
"alt-require": false,
"id-class-value": false
}
1 change: 1 addition & 0 deletions .github/workflows/linter.yml
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env:
# To report GitHub Actions status checks
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
HTMLHINT_CONFIG_FILE: .github/linters/.htmlhintrc
VALIDATE_ALL_CODEBASE: false
VALIDATE_ANSIBLE: false
VALIDATE_CHECKOV: false
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
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91 changes: 55 additions & 36 deletions docs/BreedbaseManual.tex
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5 changes: 3 additions & 2 deletions docs/basic-website-usage.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
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95 changes: 58 additions & 37 deletions docs/data-analysis-tools.html
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7 changes: 4 additions & 3 deletions docs/index.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
Expand All @@ -358,7 +359,7 @@ <h1>
<div id="header">
<h1 class="title">User Manual of Breedbase</h1>
<p class="author"><em>Breedbase team</em></p>
<p class="date"><em>2024-12-13</em></p>
<p class="date"><em>2025-02-25</em></p>
</div>
<div id="introduction" class="section level1 unnumbered hasAnchor">
<h1>Introduction<a href="index.html#introduction" class="anchor-section" aria-label="Anchor link to header"></a></h1>
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
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5 changes: 3 additions & 2 deletions docs/managing-barcodes.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
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5 changes: 3 additions & 2 deletions docs/managing-breeding-programs.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
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5 changes: 3 additions & 2 deletions docs/managing-crosses.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
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5 changes: 3 additions & 2 deletions docs/managing-downloads.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
Expand Down Expand Up @@ -334,7 +334,8 @@
<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
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5 changes: 3 additions & 2 deletions docs/managing-field-trials.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
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5 changes: 3 additions & 2 deletions docs/managing-genotyping-plates.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
</ul></li>
<li class="divider"></li>
<li><a href="https://bookdown.org/" target="blank">Published with bookdown</a></li>
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5 changes: 3 additions & 2 deletions docs/managing-image-data.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
</ul></li>
<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2024-12-13" />
<meta name="date" content="2025-02-25" />

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<li class="chapter" data-level="25.12.8" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#faq"><i class="fa fa-check"></i><b>25.12.8</b> FAQ</a></li>
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<li class="chapter" data-level="25.13" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#general-mixed-model-tool"><i class="fa fa-check"></i><b>25.13</b> General Mixed Model Tool</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gcpc"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GCPC)</a></li>
<li class="chapter" data-level="25.14" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#genomic-prediction-of-cross-performance-gpcp"><i class="fa fa-check"></i><b>25.14</b> Genomic Prediction of Cross Performance (GPCP)</a></li>
<li class="chapter" data-level="25.15" data-path="data-analysis-tools.html"><a href="data-analysis-tools.html#tool-compatibility"><i class="fa fa-check"></i><b>25.15</b> Tool Compatibility</a></li>
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