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<!DOCTYPE html>
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<head>
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<title>License</title>
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menuAnchor.parent().addClass('active');
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<h1 class="title toc-ignore">License</h1>
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<p>
<button type="button" class="btn btn-default btn-workflowr btn-workflowr-report" data-toggle="collapse" data-target="#workflowr-report">
<span class="glyphicon glyphicon-list" aria-hidden="true"></span> workflowr <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span>
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<strong>Last updated:</strong> 2020-02-25
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<p>
<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 2 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 0
</p>
<p>
<strong>Knit directory:</strong> <code>csna_workflow/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
</p>
<p>
This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis was created with <a
href="https://github.com/jdblischak/workflowr">workflowr</a> (version 1.4.0). The <em>Checks</em> tab describes the reproducibility checks that were applied when the results were created. The <em>Past versions</em> tab lists the development history.
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRMarkdownfilestronguptodate"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>R Markdown file:</strong> up-to-date </a>
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<p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomTheJacksonLaboratoryCSNAtree2fa487b82bfe428508a7f03b96b41eb8e27fcaf3targetblank2fa487ba"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/2fa487b82bfe428508a7f03b96b41eb8e27fcaf3" target="_blank">2fa487b</a> </a>
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<div class="panel-body">
<p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated. <br><br> Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
</p>
<pre><code>
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Untracked: output/m3.Novelty_resids_datarelease_07302918_genomescan.pdf
Untracked: output/m3.Novelty_resids_datarelease_12182019.RData
Untracked: output/m3.Novelty_resids_datarelease_12182019_coeffgeneplot.pdf
Untracked: output/m3.Novelty_resids_datarelease_12182019_genomescan.pdf
Untracked: output/m3.Novelty_residuals_RankNormal_datarelease_07302918.RData
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Untracked: output/m3.Novelty_residuals_RankNormal_datarelease_12182019.RData
Untracked: output/m3.Novelty_residuals_RankNormal_datarelease_12182019_coeffgeneplot.pdf
Untracked: output/m3.Novelty_residuals_RankNormal_datarelease_12182019_genomescan.pdf
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Untracked: output/number_crossover.pdf
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Unstaged changes:
Modified: README.md
Modified: _workflowr.yml
Modified: analysis/01_geneseek2qtl2.R
Modified: analysis/02_geneseek2intensity.R
Modified: analysis/03_firstgm2genoprobs.R
Modified: analysis/04_diagnosis_qc_gigamuga_nine_batches.R
Modified: analysis/06_final_pr_apr_69K.R
Modified: analysis/07.1_html_founder_prop.R
Modified: analysis/07_recomb_size_founder_prop.R
Modified: analysis/08_gcta_herit.R
Modified: analysis/09_qtlmapping.R
Modified: analysis/10_qtl_permu.R
Modified: analysis/11_qtl_blup.R
Modified: analysis/run_01_geneseek2qtl2.R
Modified: analysis/run_02_geneseek2intensity.R
Modified: analysis/run_03_firstgm2genoprobs.R
Modified: analysis/run_04_diagnosis_qc_gigamuga_nine_batches.R
Modified: analysis/run_05_after_diagnosis_qc_gigamuga_nine_batches.R
Modified: analysis/run_06_final_pr_apr_69K.R
Modified: analysis/run_07.1_html_founder_prop.R
Modified: analysis/run_07_recomb_size_founder_prop.R
Modified: analysis/run_08_gcta_herit.R
Modified: analysis/run_09_qtlmapping.R
Modified: analysis/run_10_qtl_permu.R
Modified: analysis/run_11_qtl_blup.R
</code></pre>
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