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<strong>Last updated:</strong> 2022-04-28
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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>mage_2020_marker-gene-benchmarking/</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="https://rmarkdown.rstudio.com">R Markdown</a> analysis was created with <a
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenprivatemage2020markergenebenchmarkingtree24ee16ab45272a667abbb7f97dfcbf526f8b80e3targetblank24ee16aa"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/tree/24ee16ab45272a667abbb7f97dfcbf526f8b80e3" target="_blank">24ee16a</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.
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The results in this page were generated with repository version <a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/tree/24ee16ab45272a667abbb7f97dfcbf526f8b80e3" target="_blank">24ee16a</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
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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:
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<pre><code>
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: .snakemake/
Ignored: NSForest/.Rhistory
Ignored: NSForest/NS-Forest_v3_Extended_Binary_Markers_Supplmental.csv
Ignored: NSForest/NS-Forest_v3_Full_Results.csv
Ignored: NSForest/NSForest3_medianValues.csv
Ignored: NSForest/NSForest_v3_Final_Result.csv
Ignored: NSForest/__pycache__/
Ignored: NSForest/data/
Ignored: RankCorr/picturedRocks/__pycache__/
Ignored: benchmarks/
Ignored: config/
Ignored: data/cellmarker/
Ignored: data/downloaded_data/
Ignored: data/expert_annotations/
Ignored: data/expert_mgs/
Ignored: data/raw_data/
Ignored: data/real_data/
Ignored: data/sim_data/
Ignored: data/sim_mgs/
Ignored: data/special_real_data/
Ignored: figures/
Ignored: logs/
Ignored: results/
Ignored: weights/
Untracked files:
Untracked: analysis/de-pars-sims.Rmd
Untracked: analysis/implemetation-quality.Rmd
Untracked: analysis/inter-dataset-analysis.Rmd
Untracked: analysis/lawlor-expert-analysis.Rmd
Untracked: analysis/number-selected-analysis.Rmd
Untracked: analysis/ss3-pbmc-analysis.Rmd
Untracked: analysis/ss3-pbmc-expert-analysis.Rmd
Untracked: analysis/zeisel-expert-analysis.Rmd
Untracked: analysis/zhao-data.Rmd
Untracked: code/expert-annotation-utils.R
Unstaged changes:
Modified: analysis/astrocyte-data.Rmd
Modified: analysis/cellmarker.Rmd
Modified: analysis/concordance.Rmd
Modified: analysis/direction-selected-analysis.Rmd
Modified: analysis/down-regulated-case-study.Rmd
Deleted: analysis/fdr-curves.Rmd
Modified: analysis/log-fc-values-analysis.Rmd
Modified: analysis/memory.Rmd
Modified: analysis/p-value-analysis.Rmd
Modified: analysis/pbmc3k-data.Rmd
Modified: analysis/pbmc3k-expert-analysis.Rmd
Modified: analysis/predictive-performance.Rmd
Deleted: analysis/roc.Rmd
Modified: analysis/simulation-validation-analysis.Rmd
Deleted: analysis/sparsity-analysis.Rmd
Modified: analysis/t-test-only-zero-case-study.Rmd
Modified: analysis/time.Rmd
Modified: analysis/tpr.Rmd
Modified: analysis/zero-pvalues-case-study.Rmd
Modified: code/analysis-utils.R
Modified: code/manuscript-figures.R
Modified: code/plot-utils.R
</code></pre>
<p>
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
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These are the previous versions of the repository in which changes were made to the R Markdown (<code>analysis/about.Rmd</code>) and HTML (<code>public/about.html</code>) files. If you’ve configured a remote Git repository (see <code>?wflow_git_remote</code>), click on the hyperlinks in the table below to view the files as they were in that past version.
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html
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<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/ca82ce0376f0d272dfbf5135342387dfeb6cd8d9/public/about.html" target="_blank">ca82ce0</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-02-16
</td>
<td>
Build site.
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/2863555c1b0ccc7c310f34dc03f5a1b37670b576/public/about.html" target="_blank">2863555</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-02-10
</td>
<td>
Build site.
</td>
</tr>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/1ad9d6de2a37fd0860c0aed0d70faa3221788cb7/analysis/about.Rmd" target="_blank">1ad9d6d</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-02-10
</td>
<td>
Add workflowr website
</td>
</tr>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/7971ea23851da6cfe3cf9271f03e75a5cda465bd/analysis/about.Rmd" target="_blank">7971ea2</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2020-10-25
</td>
<td>
Initial commit
</td>
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<p>TODO</p>
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