Merge pull request #235 from AlexsLemonade/sjspielman/226-figure-legend-titles

[ci skip]

This build is based on
0d5913b.

This commit was created by the following CI build and job:
https://github.com/AlexsLemonade/ScPCA-manuscript/commit/0d5913b9256ff4a452929c68030d05ab8f71b2ea/checks
https://github.com/AlexsLemonade/ScPCA-manuscript/actions/runs/20932820596

Author: sjspielman

README.md

@@ -1,7 +1,7 @@
 # Output directory containing the formatted manuscript
 
 The [`gh-pages`](https://github.com/AlexsLemonade/ScPCA-manuscript/tree/gh-pages) branch hosts the contents of this directory at <https://AlexsLemonade.github.io/ScPCA-manuscript/>.
-The permalink for this webpage version is <https://AlexsLemonade.github.io/ScPCA-manuscript/v/fae3f10ff241bf5530095c5a43b91723fd7756bc/>.
+The permalink for this webpage version is <https://AlexsLemonade.github.io/ScPCA-manuscript/v/0d5913b9256ff4a452929c68030d05ab8f71b2ea/>.
 To redirect to the permalink for the latest manuscript version at anytime, use the link <https://AlexsLemonade.github.io/ScPCA-manuscript/v/freeze/>.
 
 ## Files
@@ -35,4 +35,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc
 ## Source
 
 The manuscripts in this directory were built from
-[`fae3f10ff241bf5530095c5a43b91723fd7756bc`](https://github.com/AlexsLemonade/ScPCA-manuscript/commit/fae3f10ff241bf5530095c5a43b91723fd7756bc).
+[`0d5913b9256ff4a452929c68030d05ab8f71b2ea`](https://github.com/AlexsLemonade/ScPCA-manuscript/commit/0d5913b9256ff4a452929c68030d05ab8f71b2ea).

index.html

@@ -66,8 +66,8 @@
   <meta name="dc.date" content="2026-01-12" />
   <meta name="citation_publication_date" content="2026-01-12" />
   <meta property="article:published_time" content="2026-01-12" />
-  <meta name="dc.modified" content="2026-01-12T17:59:23+00:00" />
-  <meta property="article:modified_time" content="2026-01-12T17:59:23+00:00" />
+  <meta name="dc.modified" content="2026-01-12T19:49:35+00:00" />
+  <meta property="article:modified_time" content="2026-01-12T19:49:35+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -121,9 +121,9 @@
   <meta name="citation_fulltext_html_url" content="https://AlexsLemonade.github.io/ScPCA-manuscript/" />
   <meta name="citation_pdf_url" content="https://AlexsLemonade.github.io/ScPCA-manuscript/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://AlexsLemonade.github.io/ScPCA-manuscript/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://AlexsLemonade.github.io/ScPCA-manuscript/v/fae3f10ff241bf5530095c5a43b91723fd7756bc/" />
-  <meta name="manubot_html_url_versioned" content="https://AlexsLemonade.github.io/ScPCA-manuscript/v/fae3f10ff241bf5530095c5a43b91723fd7756bc/" />
-  <meta name="manubot_pdf_url_versioned" content="https://AlexsLemonade.github.io/ScPCA-manuscript/v/fae3f10ff241bf5530095c5a43b91723fd7756bc/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://AlexsLemonade.github.io/ScPCA-manuscript/v/0d5913b9256ff4a452929c68030d05ab8f71b2ea/" />
+  <meta name="manubot_html_url_versioned" content="https://AlexsLemonade.github.io/ScPCA-manuscript/v/0d5913b9256ff4a452929c68030d05ab8f71b2ea/" />
+  <meta name="manubot_pdf_url_versioned" content="https://AlexsLemonade.github.io/ScPCA-manuscript/v/0d5913b9256ff4a452929c68030d05ab8f71b2ea/manuscript.pdf" />
   <meta property="og:type" content="article" />
   <meta property="twitter:card" content="summary_large_image" />
   <link rel="icon" type="image/png" sizes="192x192" href="https://manubot.org/favicon-192x192.png" />
@@ -140,9 +140,9 @@ <h1 class="title">The Single-cell Pediatric Cancer Atlas: Data portal and open-s
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://AlexsLemonade.github.io/ScPCA-manuscript/v/fae3f10ff241bf5530095c5a43b91723fd7756bc/">permalink</a>)
+(<a href="https://AlexsLemonade.github.io/ScPCA-manuscript/v/0d5913b9256ff4a452929c68030d05ab8f71b2ea/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/AlexsLemonade/ScPCA-manuscript/tree/fae3f10ff241bf5530095c5a43b91723fd7756bc">AlexsLemonade/ScPCA-manuscript@fae3f10</a>
+from <a href="https://github.com/AlexsLemonade/ScPCA-manuscript/tree/0d5913b9256ff4a452929c68030d05ab8f71b2ea">AlexsLemonade/ScPCA-manuscript@0d5913b</a>
 on January 12, 2026.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -890,8 +890,8 @@ <h2 class="page_break_before" id="figure-titles-and-legends">Figure Titles and L
 <!-- Figure 2 -->
 <div id="fig:fig2" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_2.png?sanitize=true" style="width:7in" data-tag="2" alt="Figure 2: Overview of the scpca-nf workflow." />
-<figcaption aria-hidden="true"><span>Figure 2:</span> <strong>Overview of the <code>scpca-nf</code> workflow.</strong></figcaption>
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_2.png?sanitize=true" style="width:7in" data-tag="2" alt="Figure 2: Overview of the scpca-nf workflow and download file structures." />
+<figcaption aria-hidden="true"><span>Figure 2:</span> <strong>Overview of the <code>scpca-nf</code> workflow and download file structures.</strong></figcaption>
 </figure>
 </div>
 <p>A. Overview of <code>scpca-nf</code>, the primary workflow for processing single-cell and single-nuclei RNA-seq data for the ScPCA Portal.
@@ -932,8 +932,8 @@ <h2 class="page_break_before" id="figure-titles-and-legends">Figure Titles and L
 <!-- Figure 3 -->
 <div id="fig:fig3" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_3.png?sanitize=true" style="width:7in" data-tag="3" alt="Figure 3: ScPCA Portal project download file structure and merged object workflow." />
-<figcaption aria-hidden="true"><span>Figure 3:</span> <strong>ScPCA Portal project download file structure and merged object workflow.</strong></figcaption>
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_3.png?sanitize=true" style="width:7in" data-tag="3" alt="Figure 3: Consensus cell type annotation in scpca-nf." />
+<figcaption aria-hidden="true"><span>Figure 3:</span> <strong>Consensus cell type annotation in <code>scpca-nf</code>.</strong></figcaption>
 </figure>
 </div>
 <p>A. Expanded view of the process for adding cell type annotations within <code>scpca-nf</code>, as introduced in Figure <a href="#fig:fig2">2</a>A.
@@ -1093,8 +1093,8 @@ <h2 class="page_break_before" id="supplementary-figures-and-tables">Supplementar
 <!-- Figure S3 -->
 <div id="fig:figS3" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s3.png?sanitize=true" style="width:7in" data-tag="S3" alt="Figure S3: Processing other sequencing modalities with scpca-nf." />
-<figcaption aria-hidden="true"><span>Figure S3:</span> <strong>Processing other sequencing modalities with <code>scpca-nf</code>.</strong></figcaption>
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s3.png?sanitize=true" style="width:7in" data-tag="S3" alt="Figure S3: Processing other sequencing modalities and merging objects with scpca-nf." />
+<figcaption aria-hidden="true"><span>Figure S3:</span> <strong>Processing other sequencing modalities and merging objects with <code>scpca-nf</code>.</strong></figcaption>
 </figure>
 </div>
 <p>A. Overview of the bulk RNA-Seq workflow.
@@ -1446,7 +1446,7 @@ <h2 class="page_break_before" id="references">References</h2>
 <div class="csl-left-margin">92. </div><div class="csl-right-inline"><strong>Powering single-cell analyses in the browser with WebAssembly</strong> <div class="csl-block">Aaron Lun, Jayaram Kancherla</div> <em>Cold Spring Harbor Laboratory</em> (2022-03-04) <a href="https://doi.org/gtk3dc">https://doi.org/gtk3dc</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1101/2022.03.02.482701">10.1101/2022.03.02.482701</a></div></div>
 </div>
 <div id="ref-1FzXrvESX" class="csl-entry" role="doc-biblioentry">
-<div class="csl-left-margin">93. </div><div class="csl-right-inline"><a href="https://www.kanaverse.org/kana/">https://www.kanaverse.org/kana/</a></div>
+<div class="csl-left-margin">93. </div><div class="csl-right-inline"><strong>kana</strong> <a href="https://www.kanaverse.org/kana/">https://www.kanaverse.org/kana/</a></div>
 </div>
 <div id="ref-Whp3r83M" class="csl-entry" role="doc-biblioentry">
 <div class="csl-left-margin">94. </div><div class="csl-right-inline"><strong>A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics</strong> <div class="csl-block">Haoyang Li, Juexiao Zhou, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao</div> <em>Nature Communications</em> (2023-03-21) <a href="https://doi.org/gtk3c9">https://doi.org/gtk3c9</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1038/s41467-023-37168-7">10.1038/s41467-023-37168-7</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36941264">36941264</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10027878">PMC10027878</a></div></div>