d0632693bee08bf61b7990e0c6a1de8c050e337f
mspeir
  Sat Aug 1 20:53:09 2026 -0700
singleCellSignalsPeaks: color by cell class, harmonize labels and facets (hg38)

Overhaul of the hg38 track and the shared build scripts it and the mm10 track
are generated from:

- Color every subtrack by broad cell class from one colorblind-conscious palette
(shared with the mm10 track, so a class is the same color on both assemblies);
add a color legend to the description page.
- Add a "Cell class" facet; the fine cell type becomes a searchable table column.
Group subtracks by class via priority; every subtrack is off by default.
- Paper-curated cell-type names, redundant-synonym merges, QC-cluster drop, and
per-collection tissue/life-stage/condition (including the SEA-AD region and
ADNC neuropathology level, from Gabitto 2024 and Hawrylycz 2024).
- Rebuild the longLabels from the harmonized cell type + facets, so the cryptic
source short labels decode.
- Reclassify 10 mislabeled interaction bigBeds out of the signal/peaks composite,
retype a narrowPeak-format bigBed, and drop deprecated *.old data
(936 -> 925 subtracks).
- Archive the curation with the scripts: build_celltype_crosswalks.py and
celltype-crosswalks/ (per-collection crosswalks, palette, class map, and the
paper-decode source tables).

refs #37914

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html
index da1cc38351c..50f2215eb6f 100644
--- src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html
+++ src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html
@@ -63,30 +63,76 @@
     cortex; tracks are colored by SEA-AD subclass. 184 signal subtracks
     (Gabitto et al. 2024).
   </li>
 </ul>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 This is a faceted collection, so the subtracks are chosen with filter menus
 rather than a long checkbox list. Use the facets on the track configuration
 page to narrow the subtracks by dataset, tissue, life stage, condition, data
 type, assay, and cell type, then turn on the ones you want. Signal subtracks draw
 as coverage graphs and peak subtracks draw as boxes. Each subtrack links back to
 its source dataset in the Cell Browser.
 </p>
 
+<p>
+Subtracks are colored by broad cell-type class, so the same class is shown in the same color across datasets and matches the coloring of the corresponding mouse track. The classes are:
+</p>
+<table class="stdTbl">
+  <tr><th style="background-color:rgb(0,114,178);width:2em">&nbsp;</th>
+      <td>Excitatory neuron &mdash; glutamatergic neurons of the cortical layers, hippocampal CA fields and dentate gyrus, and claustrum</td></tr>
+  <tr><th style="background-color:rgb(213,94,0);width:2em">&nbsp;</th>
+      <td>Inhibitory neuron &mdash; GABAergic neurons and interneurons (Pvalb, Sst, Lamp5, and CGE- and MGE-derived types)</td></tr>
+  <tr><th style="background-color:rgb(230,159,0);width:2em">&nbsp;</th>
+      <td>Medium spiny neuron &mdash; striatal D1 and D2 projection neurons of the direct and indirect pathways</td></tr>
+  <tr><th style="background-color:rgb(86,180,233);width:2em">&nbsp;</th>
+      <td>Other neuron &mdash; remaining neuronal types, such as Cajal-Retzius cells</td></tr>
+  <tr><th style="background-color:rgb(51,34,136);width:2em">&nbsp;</th>
+      <td>Neural progenitor &mdash; neuroblasts, radial glia, and nephron progenitors</td></tr>
+  <tr><th style="background-color:rgb(0,158,115);width:2em">&nbsp;</th>
+      <td>Astrocyte &mdash; astrocytes, including Bergmann glia and fibrous and protoplasmic subtypes</td></tr>
+  <tr><th style="background-color:rgb(204,121,167);width:2em">&nbsp;</th>
+      <td>Oligodendrocyte &mdash; oligodendrocytes across the newly-formed, myelin-forming, and mature stages</td></tr>
+  <tr><th style="background-color:rgb(240,228,66);width:2em">&nbsp;</th>
+      <td>Oligodendrocyte precursor &mdash; oligodendrocyte precursor cells (OPCs) and committed precursors</td></tr>
+  <tr><th style="background-color:rgb(0,0,0);width:2em">&nbsp;</th>
+      <td>Microglia &mdash; microglia and perivascular macrophages</td></tr>
+  <tr><th style="background-color:rgb(136,204,238);width:2em">&nbsp;</th>
+      <td>Endothelial &mdash; endothelial cells of arteries, capillaries, veins, and endocardium</td></tr>
+  <tr><th style="background-color:rgb(221,204,119);width:2em">&nbsp;</th>
+      <td>Mural &mdash; pericytes, smooth muscle, and vascular leptomeningeal cells</td></tr>
+  <tr><th style="background-color:rgb(238,102,119);width:2em">&nbsp;</th>
+      <td>Immune &mdash; lymphoid (B, T) and myeloid (macrophage, dendritic, basophil) immune cells</td></tr>
+  <tr><th style="background-color:rgb(170,68,153);width:2em">&nbsp;</th>
+      <td>Erythroid &mdash; erythroid cells and erythroblasts</td></tr>
+  <tr><th style="background-color:rgb(153,153,51);width:2em">&nbsp;</th>
+      <td>Hematopoietic stem/progenitor &mdash; hematopoietic stem and progenitor cells</td></tr>
+  <tr><th style="background-color:rgb(170,68,0);width:2em">&nbsp;</th>
+      <td>Cardiomyocyte &mdash; heart muscle cells</td></tr>
+  <tr><th style="background-color:rgb(102,17,0);width:2em">&nbsp;</th>
+      <td>Muscle &mdash; skeletal muscle myofibers, satellite cells, and junctional myonuclei</td></tr>
+  <tr><th style="background-color:rgb(17,119,51);width:2em">&nbsp;</th>
+      <td>Epithelial &mdash; epithelial cells of many tissues, such as airway, gut, kidney tubule, and secretory epithelia</td></tr>
+  <tr><th style="background-color:rgb(153,79,0);width:2em">&nbsp;</th>
+      <td>Stromal &mdash; fibroblasts, mesenchymal, and other stromal cells</td></tr>
+  <tr><th style="background-color:rgb(153,153,153);width:2em">&nbsp;</th>
+      <td>Other &mdash; other or mixed cell types, such as olfactory ensheathing cells and melanocytes</td></tr>
+  <tr><th style="background-color:rgb(187,187,187);width:2em">&nbsp;</th>
+      <td>Unknown &mdash; cell type not resolved from the source data</td></tr>
+</table>
+
 <h2>Methods</h2>
 <p>
 Each dataset was produced and processed by a different group, so the assays and
 analysis pipelines vary. The signal and peak files here are the same ones served
 by the individual Cell Browser datasets, copied into the browser without change.
 The table summarizes each dataset; see the linked publication for full detail.
 </p>
 <table class="stdTbl">
   <tr><th>Dataset</th><th>Assay</th><th>Processing summary</th></tr>
   <tr>
     <td>Human Enhancer Atlas</td>
     <td>single-cell ATAC-seq (adult and fetal tissues)</td>
     <td>Accessibility profiled across 30 adult and 15 fetal tissues, integrated to call about 1.2 million candidate cis-regulatory elements across 222 cell types.</td>
   </tr>
   <tr>
@@ -141,35 +187,35 @@
 <a href="hgTables">Table Browser</a> or the
 <a href="hgIntegrator">Data Integrator</a>, and read from scripts through our
 <a href="https://api.genome.ucsc.edu" target="_blank">API</a>.
 </p>
 <p>
 For automated download and analysis, the signal and peak files are stored under
 <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/singleCellSignalsPeaks/" target="_blank">http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/singleCellSignalsPeaks/</a>,
 keeping the same per-dataset subdirectories shown on the configuration page. The
 files can be read with the command-line tools <tt>bigWigToBedGraph</tt> (for the
 signal bigWigs) and <tt>bigBedToBed</tt> (for the peak files), which can be
 compiled from source or downloaded as
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">precompiled binaries</a>.
 Both take a region so you do not have to download the whole file, for example:
 </p>
 <pre><code>bigWigToBedGraph -chrom=chr1 -start=1000000 -end=1100000 \
-  http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/singleCellSignalsPeaks/neuro-degen-atac/bigWig/neuronal-celltypes/projNeuron_LDSCgroup-VIP_Interneurons_GRanges_insertions_bin100_RIPnorm.bw \
+  http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/singleCellSignalsPeaks/cardiogenesis-atac/hub/in-vivo/Veins.bw \
   stdout
 
 bigBedToBed -chrom=chr21 -start=0 -end=48000000 \
-  http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/singleCellSignalsPeaks/cortex-atac/hub/Enhancerpeaks/AstroOligo.bb \
+  http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/singleCellSignalsPeaks/cortex-atac/hub/peaks.bb \
   stdout</code></pre>
 <p>
 The underlying matrices, metadata, and per-dataset download details are on each
 dataset's page in the <a href="https://cells.ucsc.edu" target="_blank">UCSC Cell
 Browser</a>.
 </p>
 
 <h2>Credits</h2>
 <p>
 Thanks to the UCSC Cell Browser team and the research groups whose single-cell
 datasets are shown here. Questions about a particular subtrack are best directed
 to the dataset page it links to.
 </p>
 
 <h2>References</h2>