Merge pull request #237 from AlexsLemonade/sjspielman/207-figure-links

[ci skip]

This build is based on
47a0206.

This commit was created by the following CI build and job:
https://github.com/AlexsLemonade/ScPCA-manuscript/commit/47a02063ba60a2bc1e3ebbad076885942c3d5329/checks
https://github.com/AlexsLemonade/ScPCA-manuscript/actions/runs/20962528004

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/7e4d9053d8d1d2619806ef331d98138dededdac8/>.
+The permalink for this webpage version is <https://AlexsLemonade.github.io/ScPCA-manuscript/v/47a02063ba60a2bc1e3ebbad076885942c3d5329/>.
 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
-[`7e4d9053d8d1d2619806ef331d98138dededdac8`](https://github.com/AlexsLemonade/ScPCA-manuscript/commit/7e4d9053d8d1d2619806ef331d98138dededdac8).
+[`47a02063ba60a2bc1e3ebbad076885942c3d5329`](https://github.com/AlexsLemonade/ScPCA-manuscript/commit/47a02063ba60a2bc1e3ebbad076885942c3d5329).

index.html

@@ -66,8 +66,8 @@
   <meta name="dc.date" content="2026-01-13" />
   <meta name="citation_publication_date" content="2026-01-13" />
   <meta property="article:published_time" content="2026-01-13" />
-  <meta name="dc.modified" content="2026-01-13T14:04:23+00:00" />
-  <meta property="article:modified_time" content="2026-01-13T14:04:23+00:00" />
+  <meta name="dc.modified" content="2026-01-13T15:33:55+00:00" />
+  <meta property="article:modified_time" content="2026-01-13T15:33:55+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/7e4d9053d8d1d2619806ef331d98138dededdac8/" />
-  <meta name="manubot_html_url_versioned" content="https://AlexsLemonade.github.io/ScPCA-manuscript/v/7e4d9053d8d1d2619806ef331d98138dededdac8/" />
-  <meta name="manubot_pdf_url_versioned" content="https://AlexsLemonade.github.io/ScPCA-manuscript/v/7e4d9053d8d1d2619806ef331d98138dededdac8/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://AlexsLemonade.github.io/ScPCA-manuscript/v/47a02063ba60a2bc1e3ebbad076885942c3d5329/" />
+  <meta name="manubot_html_url_versioned" content="https://AlexsLemonade.github.io/ScPCA-manuscript/v/47a02063ba60a2bc1e3ebbad076885942c3d5329/" />
+  <meta name="manubot_pdf_url_versioned" content="https://AlexsLemonade.github.io/ScPCA-manuscript/v/47a02063ba60a2bc1e3ebbad076885942c3d5329/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/7e4d9053d8d1d2619806ef331d98138dededdac8/">permalink</a>)
+(<a href="https://AlexsLemonade.github.io/ScPCA-manuscript/v/47a02063ba60a2bc1e3ebbad076885942c3d5329/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/AlexsLemonade/ScPCA-manuscript/tree/7e4d9053d8d1d2619806ef331d98138dededdac8">AlexsLemonade/ScPCA-manuscript@7e4d905</a>
+from <a href="https://github.com/AlexsLemonade/ScPCA-manuscript/tree/47a02063ba60a2bc1e3ebbad076885942c3d5329">AlexsLemonade/ScPCA-manuscript@47a0206</a>
 on January 13, 2026.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -888,7 +888,7 @@ <h2 class="page_break_before" id="figure-titles-and-legends">Figure Titles and L
 <!-- Figure 1 -->
 <div id="fig:fig1" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_1.png?sanitize=true" style="width:7in" data-tag="1" alt="Figure 1: Overview of ScPCA Portal contents." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_1.png?sanitize=true" style="width:7in" data-tag="1" alt="Figure 1: Overview of ScPCA Portal contents." />
 <figcaption aria-hidden="true"><span>Figure 1:</span> <strong>Overview of ScPCA Portal contents.</strong></figcaption>
 </figure>
 </div>
@@ -910,7 +910,7 @@ <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 and download file structures." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/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>
@@ -952,7 +952,7 @@ <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: Consensus cell type annotation in scpca-nf." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/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>
@@ -975,7 +975,7 @@ <h2 class="page_break_before" id="figure-titles-and-legends">Figure Titles and L
 <!-- Figure 4 -->
 <div id="fig:fig4" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_5.png?sanitize=true" style="width:7in" data-tag="4" alt="Figure 4: Consensus cell type annotations in Brain and CNS tumors." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_4.png?sanitize=true" style="width:7in" data-tag="4" alt="Figure 4: Consensus cell type annotations in Brain and CNS tumors." />
 <figcaption aria-hidden="true"><span>Figure 4:</span> <strong>Consensus cell type annotations in Brain and CNS tumors.</strong></figcaption>
 </figure>
 </div>
@@ -1002,7 +1002,7 @@ <h2 class="page_break_before" id="figure-titles-and-legends">Figure Titles and L
 <!-- Figure 5 -->
 <div id="fig:fig5" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_5.png?sanitize=true" style="width:7in" data-tag="5" alt="Figure 5: Cell type annotation and CNV inference on neuroblastoma samples." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_5.png?sanitize=true" style="width:7in" data-tag="5" alt="Figure 5: Cell type annotation and CNV inference on neuroblastoma samples." />
 <figcaption aria-hidden="true"><span>Figure 5:</span> <strong>Cell type annotation and CNV inference on neuroblastoma samples.</strong></figcaption>
 </figure>
 </div>
@@ -1022,7 +1022,7 @@ <h2 class="page_break_before" id="figure-titles-and-legends">Figure Titles and L
 <!-- Figure 6 -->
 <div id="fig:fig6" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_6.png?sanitize=true" style="width:7in" data-tag="6" alt="Figure 6: Comparison of bulk and pseudobulk modalities." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_6.png?sanitize=true" style="width:7in" data-tag="6" alt="Figure 6: Comparison of bulk and pseudobulk modalities." />
 <figcaption aria-hidden="true"><span>Figure 6:</span> <strong>Comparison of bulk and pseudobulk modalities.</strong></figcaption>
 </figure>
 </div>
@@ -1059,7 +1059,7 @@ <h2 class="page_break_before" id="supplementary-figures-and-tables">Supplementar
 <!-- Figure S1 -->
 <div id="fig:figS1" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s1.png?sanitize=true" style="width:7in" data-tag="S1" alt="Figure S1: Results from benchmarking alevin-fry and CellRanger performance." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s1.png?sanitize=true" style="width:7in" data-tag="S1" alt="Figure S1: Results from benchmarking alevin-fry and CellRanger performance." />
 <figcaption aria-hidden="true"><span>Figure S1:</span> <strong>Results from benchmarking <code>alevin-fry</code> and <code>CellRanger</code> performance.</strong></figcaption>
 </figure>
 </div>
@@ -1081,7 +1081,7 @@ <h2 class="page_break_before" id="supplementary-figures-and-tables">Supplementar
 <!-- Figure S2 -->
 <div id="fig:figS2" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s2.png?sanitize=true" style="width:7in" data-tag="S2" alt="Figure S2: Processing additional single-cell modalities in scpca-nf." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s2.png?sanitize=true" style="width:7in" data-tag="S2" alt="Figure S2: Processing additional single-cell modalities in scpca-nf." />
 <figcaption aria-hidden="true"><span>Figure S2:</span> <strong>Processing additional single-cell modalities in <code>scpca-nf</code>.</strong></figcaption>
 </figure>
 </div>
@@ -1113,7 +1113,7 @@ <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 and merging objects with scpca-nf." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/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>
@@ -1136,7 +1136,7 @@ <h2 class="page_break_before" id="supplementary-figures-and-tables">Supplementar
 <!--Figure S4-->
 <div id="fig:figS4" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s4.png?sanitize=true" style="width:7in" data-tag="S4" alt="Figure S4: Ontology-aware consensus cell type assignment provides harmonized labels for cells." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s4.png?sanitize=true" style="width:7in" data-tag="S4" alt="Figure S4: Ontology-aware consensus cell type assignment provides harmonized labels for cells." />
 <figcaption aria-hidden="true"><span>Figure S4:</span> <strong>Ontology-aware consensus cell type assignment provides harmonized labels for cells.</strong></figcaption>
 </figure>
 </div>
@@ -1151,7 +1151,7 @@ <h2 class="page_break_before" id="supplementary-figures-and-tables">Supplementar
 <!-- Figure S5 -->
 <div id="fig:figS5" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s6.png?sanitize=true" style="width:9in" data-tag="S5" alt="Figure S5: Consensus cell type annotation gene expression in other diagnosis groups." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s5.png?sanitize=true" style="width:9in" data-tag="S5" alt="Figure S5: Consensus cell type annotation gene expression in other diagnosis groups." />
 <figcaption aria-hidden="true"><span>Figure S5:</span> <strong>Consensus cell type annotation gene expression in other diagnosis groups.</strong></figcaption>
 </figure>
 </div>
@@ -1164,7 +1164,7 @@ <h2 class="page_break_before" id="supplementary-figures-and-tables">Supplementar
 <!-- Figure S6 -->
 <div id="fig:figS6" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s7.png?sanitize=true" style="width:7in" data-tag="S6" alt="Figure S6: *Consensus cell type annotation distributions in other diagnosis groups." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s6.png?sanitize=true" style="width:7in" data-tag="S6" alt="Figure S6: *Consensus cell type annotation distributions in other diagnosis groups." />
 <figcaption aria-hidden="true"><span>Figure S6:</span> *<strong>Consensus cell type annotation distributions in other diagnosis groups.</strong></figcaption>
 </figure>
 </div>
@@ -1175,7 +1175,7 @@ <h2 class="page_break_before" id="supplementary-figures-and-tables">Supplementar
 <!-- Figure S7 -->
 <div id="fig:figS7" class="fignos">
 <figure>
-<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.1.1/figures/compiled_figures/pngs/figure_s8.png?sanitize=true" style="width:7in" data-tag="S7" alt="Figure S7: Comparison of bulk and pseudobulk modalities for additional projects." />
+<img src="https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/v0.2.0/figures/compiled_figures/pngs/figure_s7.png?sanitize=true" style="width:7in" data-tag="S7" alt="Figure S7: Comparison of bulk and pseudobulk modalities for additional projects." />
 <figcaption aria-hidden="true"><span>Figure S7:</span> <strong>Comparison of bulk and pseudobulk modalities for additional projects.</strong></figcaption>
 </figure>
 </div>