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<!DOCTYPE html>
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<strong>Last updated:</strong> 2021-06-16
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<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
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<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>
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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 1.6.2). 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="#strongRepositoryversionstrongahrefhttpsgithubcomTheJacksonLaboratoryCSNAtree33b7fb8d10698090afcddf54344dba42bf8cb60etargetblank33b7fb8a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/33b7fb8d10698090afcddf54344dba42bf8cb60e" target="_blank">33b7fb8</a> </a>
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Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
The results in this page were generated with repository version <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/33b7fb8d10698090afcddf54344dba42bf8cb60e" target="_blank">33b7fb8</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
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>
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Untracked files:
Untracked: analysis/.nfs0000000135a08b9b00002448
Untracked: analysis/.nfs0000000135a08ba50000244a
Untracked: analysis/csna_image.sif
Untracked: analysis/index0.Rmd
Untracked: analysis/ped.R
Untracked: analysis/qtlmapping_results.Rmd
Untracked: analysis/rstudio.4.0.3.simg
Untracked: analysis/scripts/
Untracked: analysis/workflow_proc.R
Untracked: analysis/workflow_proc.sh
Untracked: analysis/workflow_proc.stderr
Untracked: analysis/workflow_proc.stdout
Untracked: archived/
Untracked: code/FinalReport2Plink.sh
Untracked: code/csna_qtlmapping_plot.R
Untracked: code/csna_qtlmapping_workflow.R
Untracked: code/csna_snp_gwas.R
Untracked: code/do2sanger.helper.R
Untracked: code/plink-1.07-x86_64.zip
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Untracked: code/predict_sanger_snp_geno.R
Untracked: code/pylmm/
Untracked: code/reconst_utils.R
Untracked: data/69k_grid_pgmap.RData
Untracked: data/FinalReport/
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Untracked: data/GM/
Untracked: data/Jackson_Lab_11_batches/
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Untracked: data/Jackson_Lab_Bubier_MURGIGV01/
Untracked: data/Jackson_Lab_Gagnon/
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Untracked: data/cc_do_founders_key.rds
Untracked: data/cc_variants.sqlite
Untracked: data/gene.anno.cis.RData
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Untracked: data/mouse_genes_mgi.sqlite
Untracked: data/pheno/
Untracked: output/DO.allrawpheno.corr.fullmat.RData
Untracked: output/archived_output/
Untracked: output/circle_chromosome.pdf
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Untracked: output/qtlmapping.heatmap.sens.pdf
Untracked: output/qtlmapping/
Untracked: output/qtlmapping_plot/
Untracked: output/snp_gwas/
Unstaged changes:
Modified: .Rprofile
Modified: .gitignore
Modified: README.md
Modified: _workflowr.yml
Modified: analysis/00_Process_all_phenotypes_in_founder_CC_DO.Rmd
Deleted: analysis/01_geneseek2qtl2.R
Deleted: analysis/02_geneseek2intensity.R
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Modified: output/README.md
</code></pre>
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