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Jeffrey Pullin authoredJeffrey Pullin authored
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<h1 class="title toc-ignore">A comparison of marker gene selection methods for single-cell RNA sequencing data</h1>
<h4 class="author">Jeffrey Pullin, Davis McCarthy</h4>
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<strong>Last updated:</strong> 2022-05-11
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Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/f0da1adeaa79904892636925494156cc39f9b2bd/analysis/index.Rmd" target="_blank">f0da1ad</a>
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<td>
Jeffrey Pullin
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2022-05-11
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Update landing page
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html
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/0e478744e8ae38da36e2de4468dbb4ec20713e84/public/index.html" target="_blank">0e47874</a>
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Jeffrey Pullin
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2022-05-04
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Build site.
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/b5045c17622cba096aca49027fd246f8930b1488/public/index.html" target="_blank">b5045c1</a>
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Jeffrey Pullin
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2022-05-02
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Build site.
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Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/048156f6817e67cc87578a17b0f30755c3044019/analysis/index.Rmd" target="_blank">048156f</a>
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Jeffrey Pullin
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2022-05-02
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Tweak analysis outputs
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Jeffrey Pullin
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2022-05-02
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Tweak analysis outputs
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html
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/8b989e1e0553365ef45bb4cd5f80865c9639af43/public/index.html" target="_blank">8b989e1</a>
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Jeffrey Pullin
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2022-05-02
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Build site.
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/05482732a2dc18f0786db385f457a99bd7d191db/public/index.html" target="_blank">0548273</a>
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<td>
Jeffrey Pullin
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2022-05-02
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Build site.
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Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/50bca7c1f36680d5fcb00fbe642d0cf576795269/analysis/index.Rmd" target="_blank">50bca7c</a>
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<td>
Jeffrey Pullin
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2022-05-02
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workflowr::wflow_publish(all = TRUE, republish = TRUE)
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<td><a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/50bca7c1f36680d5fcb00fbe642d0cf576795269/public/index.html" target="_blank">50bca7c</a>
</td>
<td>
Jeffrey Pullin
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<td>
2022-05-02
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workflowr::wflow_publish(all = TRUE, republish = TRUE)
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/5cc008f68e2dc2841fa7bbf645dd7e29515a3f0c/public/index.html" target="_blank">5cc008f</a>
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Jeffrey Pullin
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2022-02-09
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Build site.
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Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/d1aca16c0d03c5b27db12af526cfd75ea2609cea/analysis/index.Rmd" target="_blank">d1aca16</a>
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Jeffrey Pullin
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<td>
2022-02-09
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Refresh website
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/d1aca16c0d03c5b27db12af526cfd75ea2609cea/public/index.html" target="_blank">d1aca16</a>
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Jeffrey Pullin
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2022-02-09
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Refresh website
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/a1169677fc20d1c0df5d2fd8c73d7177b8823d91/public/index.html" target="_blank">a116967</a>
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Jeffrey Pullin
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2021-04-13
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Build site.
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Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/581627b1ded8649658611cb2e797da2723a0f5d1/analysis/index.Rmd" target="_blank">581627b</a>
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<td>
Jeffrey Pullin
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<td>
2021-04-13
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Rebuild index
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html
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/ca82ce0376f0d272dfbf5135342387dfeb6cd8d9/public/index.html" target="_blank">ca82ce0</a>
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Jeffrey Pullin
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2021-02-16
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Build site.
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Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/63bce665856cac94a540db0429dc46bfbb659270/analysis/index.Rmd" target="_blank">63bce66</a>
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<td>
Jeffrey Pullin
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<td>
2021-02-16
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Add new marker gene type analysis and update FDR + TPR
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html
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<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/2863555c1b0ccc7c310f34dc03f5a1b37670b576/public/index.html" target="_blank">2863555</a>
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<td>
Jeffrey Pullin</td>
<td>
2021-02-10
</td>
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Build site.
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Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/1ad9d6de2a37fd0860c0aed0d70faa3221788cb7/analysis/index.Rmd" target="_blank">1ad9d6d</a>
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<td>
Jeffrey Pullin
</td>
<td>
2021-02-10
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Add workflowr website
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Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking/blob/7971ea23851da6cfe3cf9271f03e75a5cda465bd/analysis/index.Rmd" target="_blank">7971ea2</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2020-10-25
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Initial commit
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</div>
<div id="project-overview" class="section level2">
<h2>Project overview</h2>
<p>This project aim to benchmark current methods for the selection of cell-type maker genes in scRNA-seq data. Our findings are summarized in the following preprint:</p>
<blockquote>
<p>A comparison of marker gene selection methods for single-cell RNA sequencing data<br />
Jeffrey M Pullin, Davis J McCarthy<br />
bioRxiv 2022.05.09.490241; doi: <a href="https://doi.org/10.1101/2022.05.09.490241" class="uri">https://doi.org/10.1101/2022.05.09.490241</a></p>
</blockquote>
</div>
<div id="analyses" class="section level2">
<h2>Analyses</h2>
<div id="method-comparison" class="section level3">
<h3>Method comparison</h3>
<p>We assessed the method’s</p>
<ul>
<li><a href="concordance.html">Concordance</a> (pairwise and overall)</li>
<li><a href="p-value-analysis.html">Returned p-values</a></li>
<li><a href="direction-selected-analysis.html">Regulation direction biases</a></li>
</ul>
<p>We compared the method’s performance using both simulated and real datasets on</p>
<ul><li><a href="tpr.html">Simulated marker gene performance</a></li>
<li><a href="predictive-performance.html">Predictive performance</a></li>
</ul>
<p>and ability to select expert-annotated marker genes in different datasets:</p>
<ul>
<li><a href="pbmc3k-expert-analysis.html">pbmc3k dataset</a></li>
<li><a href="lawlor-expert-analysis.html">Lawlor dataset</a></li>
<li><a href="ss3-pbmc-expert-analysis.html">SMART-seq3 dataset</a></li>
<li><a href="zeisel-expert-analysis.html">Zeisel dataset</a></li>
</ul>
<p>We additionally assessed the method’s</p>
<ul>
<li><a href="time.html">Speed</a></li>
<li><a href="memory.html">Memory usage</a></li>
<li><a href="implemetation-quality.html">Implementation quality</a></li>
</ul>
</div>
<div id="supportimg-analyses" class="section level3">
<h3>Supportimg analyses</h3>
<ul>
<li><a href="inter-dataset-analysis.html">Dataset features</a></li>
<li><a href="de-pars-sims.html">Different simulation parameters</a></li>
<li><a href="simulation-validation-analysis.html">Simulation validation analyses</a></li>
</ul>
</div>
<div id="case-studies" class="section level3">
<h3>Case studies</h3>
<p>We used specific case studies to illustrate specific issues and inconsistencies with methods, especially those implemented in the scran, Scanpy and Seurat packages.</p>
<ul>
<li><a href="zero-pvalues-case-study.html">Zero p-values</a></li>
<li><a href="double-dipping-analysis.html">Double dipping consequences</a></li>
<li><a href="log-fc-values-analysis.html">Log fold change values analysis</a></li>
<li><a href="t-test-only-zero-case-study.html">Welch t-test with only zeros case study</a></li>
<li><a href="welch-ranking-case-study.html">Welch t-test ranking case study</a></li>
<li><a href="classical-robustness-case-study.html">Classical robustness case study</a></li>
<li><a href="scran-any-case-study.html">Scran ‘any’ case study</a></li>
<li><a href="pertubation-case-study.html">Data pertubation case study</a></li>
<li><a href="seurat-method-analysi.html">Seurat method analysis case study</a></li>
<li><a href="down-regulated-case-study.html">Down-regulated case study</a></li>
<li><a href="nk-case-study.html">Natural killer cells case study</a></li>
</ul>
</div>
<div id="datasets" class="section level3">
<h3>Datasets</h3>
<p>A variety of scRNA-seq datasets are used in the used to compare methods. For theses datasets we have performed general analysis, including selecting marker genes. The code used to process the each dataset can be found in the corresponding <code>prep_*</code> R script in the <code>code</code> directory.</p>
<ul>
<li><a href="astrocyte-data.html">Astrocyte data</a></li>
<li><a href="lawlor-data.html">Lawlor data</a></li>
<li><a href="zeisel-data.html">Zeisel data</a></li>
<li><a href="pbmc3k-data.html">pbmc3k data</a></li>
<li><a href="zhao-data.html">Zhao data</a></li>
</ul>
</div>
<div id="other-analyses" class="section level3">
<h3>Other analyses</h3>
<ul>
<li><a href="single-cell-database-analysis.html">Single cell databases</a></li>
</ul>
<hr />
<p><a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International License</a>.</p>
</div>
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