b914d581f876d486caf9404e715e4f61ada38195 mspeir Mon Aug 3 16:19:44 2026 -0700 singleCellSignalsPeaks: make every subtrack label unique, fix cell-class regressions The harmonized labels were not distinguishing tracks. build_long_label composed from cell type + condition + tissue, but the upstream steps discard the discriminators on purpose to keep the facets compact, so hg38 had 925 subtracks sharing only 401 distinct longLabels and mm10 629 sharing 359. Worst case: cortex-atac's MACS, enhancer and cell-type-specific peak sets all read "Astrocytes and oligodendrocytes (Cortex ATAC)", with the peak method surviving only in the raw shortLabel. Labels are now built from the harmonized cell type plus a variant descriptor that recovers what was dropped (peak method, grouping level, cohort, signal vs peaks), and anything still colliding is qualified with its source cluster code. shortLabels are rebuilt too -- the old ones were raw source strings up to 50 chars with underscores, ArchR filename tails and R-mangled names -- abbreviated through a curated word table to 22 chars, with compact tokens where the longLabel distinction would otherwise be invisible (SEA-AD region + ADNC, CATLAS aging age). All 925/587 longLabels are now unique; no shortLabel exceeds 22 chars or contains an underscore. Also fixed, found while verifying the above: - Correcting source misspellings in the cell types broke the curated lookups, which are keyed on those same misspelled strings, and 16 hg38 tracks silently lost their Cell_class and color. The class map and the hub_config tables now normalize their keys on load, and a cell type with no broad class is reported instead of becoming "unknown". - Nephron progenitor was classed as Neural progenitor: the decode tables give it the bare broad class "Progenitor" and that was blanket-mapped to neural. It is Six2+ kidney cap mesenchyme, so it is now Stromal. The HTML legend had been worded to match the bug. - The plural/case merge picked the most frequent form, which was inconsistent -- singular for 15 of 17 merged groups but plural for Megakaryocytes/Oligodendrocytes. It now prefers the singular. - Removed 42 byte-identical Allen basal-ganglia bigWigs (md5-verified) that were served from four grouping directories and rendered as four indistinguishable mm10 subtracks, freeing 4.4 GB. Where the four copies genuinely differ all are kept and told apart by the grouping-level descriptor. mm10 goes 629 -> 587 subtracks. - Corrected five stale per-dataset subtrack counts in the description pages and spelled out what ADNC means, noting that it grades neuropathology rather than symptoms. - The SEA-AD Dataset facet link used the collection name, which is not a served Cell Browser slug; it now points at sea-ad-mtg+cohort. - Dropped a dead placeholder variable and made the hardcoded hub-build path overridable. refs #37914 Co-Authored-By: Claude Opus 5 (1M context) diff --git src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html index 50f2215eb6f..9ae0f7f1436 100644 --- src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html +++ src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html @@ -9,42 +9,42 @@ heart, and retina.

The subtracks come from these datasets:

Display Conventions and Configuration

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.

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+Most subtracks are marked Healthy in the condition facet. The SEA-AD brain +tracks instead carry an ADNC level, short for Alzheimer's disease neuropathological +change. This is the NIA-AA score that combines the anatomical distribution of amyloid +plaques (Thal phase), the stage of neurofibrillary tangle spread (Braak stage), and +neuritic plaque density (CERAD) into four ordinal levels, shown here as ADNC 0 (no AD), +ADNC 1 (low), ADNC 2 (intermediate), and ADNC 3 (high). ADNC grades neuropathology +rather than symptoms: donors with high ADNC do not necessarily have dementia, and +SEA-AD records cognitive status as a separate measure. +

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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:

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  Excitatory neuron — glutamatergic neurons of the cortical layers, hippocampal CA fields and dentate gyrus, and claustrum
  Inhibitory neuron — GABAergic neurons and interneurons (Pvalb, Sst, Lamp5, and CGE- and MGE-derived types)
  Medium spiny neuron — striatal D1 and D2 projection neurons of the direct and indirect pathways
  Other neuron — remaining neuronal types, such as Cajal-Retzius cells
 Neural progenitor — neuroblasts, radial glia, and nephron progenitors
Neural progenitor — neuroblasts, radial glia, and other neural progenitors
  Astrocyte — astrocytes, including Bergmann glia and fibrous and protoplasmic subtypes
  Oligodendrocyte — oligodendrocytes across the newly-formed, myelin-forming, and mature stages
  Oligodendrocyte precursor — oligodendrocyte precursor cells (OPCs) and committed precursors
  Microglia — microglia and perivascular macrophages
  Endothelial — endothelial cells of arteries, capillaries, veins, and endocardium
  Mural — pericytes, smooth muscle, and vascular leptomeningeal cells
  Immune — lymphoid (B, T) and myeloid (macrophage, dendritic, basophil) immune cells