3522a9acc8256a35230b07f2e7ab3fc08c827f33 mspeir Sat Sep 5 17:19:20 2026 -0700 singleCellSignalsPeaks: correct the hg38 description page counts and cite BrainVar, refs #38219 From the v503 code review. Commit 3aac3982aa2 dropped 5 hg38 subtracks and updated the makeDoc, but the dataset list on the description page was missed, so the page disagreed with both the .ra and the facet menu: - Risk Loci in Alzheimer's and Parkinson's: 1 peak subtrack, not 2 (neuro-degen-atac/peaks.bb was the one dropped) - BrainVar: 9 signal subtracks, not 13, and the text still described tracks "for all nuclei together" -- the 4 combined-stage tracks are exactly the ones dropped, so every remaining BrainVar track carries a life stage Counts re-derived from the .ra by type (bigWig = signal, else peak): the other 7 hg38 datasets and all 9 mm10 datasets were already right, 929 and 587 total. BrainVar was also the only hg38 dataset with no citation, while its methods text had grown quite specific. It now cites Werling et al. 2020, which described the cohort, with the caveat that the single-nucleus data shown here were not part of that paper -- the same distinction the Cell Browser desc.conf makes. Citing it bare would credit a bulk RNA-seq and WGS study for 10x Multiome data. References are alphabetical, so hg38 is now 10 and mm10 still 7. copySingleCellSignalsPeaksFiles.py: colors_json() reads the palette in a with block, and a malformed R,G,B row now raises the SystemExit the rest of the file uses, naming the file, line number and offending field, instead of a bare ValueError or TypeError from int() or the %02X format. Output is unchanged. makeDoc: the mm10 cell-class note now records that the bare "Progenitor" row in celltype-class.tsv is live rather than leftover -- build_stanzas' class_key() collapses plurals, so BrainVar's "Progenitors" looks up under the singular key and takes its class and color from that one row. Retiring or qualifying the row would grey out that track. A non-neural label needs a specific cell type added instead, which is how "Nephron progenitors" comes out Stromal. Also fixed a contradiction there: the file claimed celltype-class.tsv is built by build_celltype_crosswalks.py a hundred lines above the note saying, correctly, that it is hand-curated and not generated. The submitters confirmed BrainVar is 100 bp tiles, so the 1 kb in their methods text is an error and the page is right; recorded in the hg38 makeDoc. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt index 5c03f9d69e2..9ca0110387d 100644 --- src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt +++ src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt @@ -162,19 +162,29 @@ # multiomic-human-heart (40), cardiogenesis-atac (19), olg-eae-ms (18), # brainvar (9). Mislabeled interaction bigBeds (cortex-atac interact.old/) are # reclassified to the interact composite and QC clusters are dropped before the # .ra is written. Facet metadata rows match the subtracks 1:1. # All 929 longLabels are unique; shortLabels are <=22 chars with no underscores. # Every subtrack has a broad cell class and a palette color (0 unclassified). # One track legitimately shows class "Unknown": neuro-degen-atac's cluster whose # source label is literally "Unannotated". That is a real palette class, not a # classification failure. # # brainvar went 4 -> 13 subtracks when the group sent stage-split pseudobulk # coverage: 5 prenatal and 4 postnatal added alongside the 4 original # combined-stage tracks. Progenitors are prenatal only, so 9 new files, not 10. # The 4 combined-stage tracks were then dropped (section 1b), leaving the 9 # stage-split ones, so every BrainVar track is now prenatal or postnatal. +# The description page's dataset list lagged that drop by one commit: it still +# said 13 BrainVar signal subtracks and "all nuclei together and ... prenatal and +# postnatal separately", and 2 neuro-degen-atac peak subtracks. Corrected to 9 and +# 1, with the combined-stage wording removed. BrainVar was also the only hg38 +# dataset with no citation; it now cites Werling et al. 2020, which described the +# cohort, with the caveat that the single-nucleus data shown here were not part of +# that paper (the Cell Browser desc.conf makes the same distinction). hg38 is now +# 10 references, mm10 still 7. +# # Their methods text says "a tile size of 1 kb" but the data is 100 bp (every # interval is 100 bp wide on 100 bp boundaries, matching the TileSize-100 -# filenames); 100 bp is what the description page states. Worth confirming with -# them which they intended. +# filenames). The submitters confirmed 100 bp on 2026-09-05, so the 1 kb in their +# methods text is an error and the description page's 100 bp is right. No change +# needed to the page or the data.