Commits for mspeir
switch to files view, user index
v502_preview to v502_preview2 (2026-07-27 to 2026-08-04) v502
Show details
91df4233e1ec4523f20367104bbdebd932f6e640 Sat Aug 1 20:45:29 2026 -0700
- Reposition and enlarge call-outs on the Add Custom Tracks annotated image
Moved the red 'Send the data...' call-out to the empty page area right of the
Submit button, dropped the blue documentation call-out down next to the
Optional track documentation input, aligned the purple call-out with the paste
box, and enlarged the call-out text so it matches the pt2 image on the page.
refs #37355
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- src/hg/htdocs/images/tutorialImages/hgCustomAnnotated_pt1.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
d0632693bee08bf61b7990e0c6a1de8c050e337f 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>
- src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt - lines changed 16, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/build_celltype_crosswalks.py - lines changed 137, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/allen-basal-ganglia-atac.tsv - lines changed 46, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/catlas-mouse-aging.tsv - lines changed 234, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/catlas-mouse-brain.tsv - lines changed 160, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/catlas-paired-tag.tsv - lines changed 21, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/celltype-class.tsv - lines changed 342, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/celltype-palette.tsv - lines changed 22, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/clean5.tsv - lines changed 42, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/paper-decodes/hg38_ct_class.tsv - lines changed 199, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/paper-decodes/xwalk_allen-basal-ganglia-atac.tsv - lines changed 47, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/paper-decodes/xwalk_catlas-mouse-aging.tsv - lines changed 235, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/paper-decodes/xwalk_catlas-mouse-brain.tsv - lines changed 161, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/paper-decodes/xwalk_catlas-paired-tag.tsv - lines changed 22, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/paper-decodes/xwalk_clean5.tsv - lines changed 43, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/sea-ad-celltype-crosswalk.tsv - lines changed 37, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/copySingleCellSignalsPeaksFiles.py - lines changed 94, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py - lines changed 77, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html - lines changed 48, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.ra - lines changed 3783, context: html, text, full: html, text
0abed78024d40b506c2b2e3a49ad483045bc5e1d Sat Aug 1 20:53:25 2026 -0700
- singleCellSignalsPeaks: add native mm10 track
mm10 counterpart of the hg38 track: 629 single-cell ATAC signal (bigWig) and
peak (bigNarrowPeak) subtracks from 9 Cell Browser datasets, re-parented under
one faceted composite in the regulation group. Colored by broad cell class from
the same palette as hg38, grouped by class, off by default; cell types are
paper-curated and the facets/longLabels are harmonized (see the makeDoc).
Data lives in /hive/data/genomes/mm10/bed/singleCellSignalsPeaks and is served
via the /gbdb/mm10/bbi symlink; the .ra is regenerated by
makeSingleCellSignalsPeaksRa.py from the Cell Browser hub build. Included in
mm10 trackDb.ra (alpha).
refs #37914
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/mm10/singleCellSignalsPeaks.txt - lines changed 124, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html - lines changed 318, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.ra - lines changed 6864, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text
981342c978baf2d56a1ddad178b100138b55298c Sat Aug 1 20:58:19 2026 -0700
- Fix pandoc rendering of tutorial step text inside the walkthrough columns
Indented markdown that ran directly into a closing </div> was being folded
into the raw-HTML block, so Step 1 paragraphs lost their <p> wrapper (and hugged
the heading) and two Table Browser lists did not close cleanly. Added the blank
line pandoc needs before </div> in the affected columns.
refs #37355
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- docs/tutorials/customTrackTutorial.md - lines changed 2, context: html, text, full: html, text
- docs/tutorials/tableBrowserTutorial.md - lines changed 3, context: html, text, full: html, text
fd37b0cc737fd221a94034202db5458d954614eb Mon Aug 3 14:50:37 2026 -0700
- Fix mismatched heading tag in gb101 tutorial
The Interactive Tutorial panel opened an <h3> but closed with </h4>.
refs #37355
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- docs/tutorials/gb101.md - lines changed 1, context: html, text, full: html, text
93ee577eacf6c0ec157f11aee34085f34d476b72 Mon Aug 3 15:30:22 2026 -0700
- Add Recommended Track Sets and Share a link sections to gb101 tutorial
Document two features now on the RR that the intro page did not cover: the
Recommended Track Sets dialog (curated, pre-configured track groups) and the
Share a link button for short, permanent view links. Adds a screenshot of each
dialog and notes Recommended Track Sets in the Genome Browser menu list.
refs #37355
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- docs/tutorials/gb101.md - lines changed 50, context: html, text, full: html, text
- src/hg/htdocs/images/recommendedTrackSets.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/images/shareLinkExample.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
b914d581f876d486caf9404e715e4f61ada38195 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) <noreply@anthropic.com>
- src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt - lines changed 20, context: html, text, full: html, text
- src/hg/makeDb/doc/mm10/singleCellSignalsPeaks.txt - lines changed 90, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/build_celltype_crosswalks.py - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/celltype-class.tsv - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/clean5.tsv - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/paper-decodes/hg38_ct_class.tsv - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/copySingleCellSignalsPeaksFiles.py - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html - lines changed 14, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.ra - lines changed 1473, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.ra - lines changed 1735, context: html, text, full: html, text
switch to files view, user index
