Commits for gperez2

v498_preview to v498_preview2 (2026-04-27 to 2026-05-04) v498

6c22604d52ab423f3b84eb10a3d5e5bf64ce90a1 Wed Apr 29 12:31:41 2026 -0700

• mm10 ENCODE4 cCREs QA cleanups from qa-track SKILL.md pass: urlLabel trailing colon on 17 subtracks, pennantIcon simplified to text-only, removed broken encode4Reg links, plus minor description page fixes (heading case, en-dash, target="_blank", bigWigToWig in example, cgi-bin path). refs #37131 refs #37409
  • src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/cCREsSuper.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/coreCollection.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4.ccres.ra - lines changed 19, context: html, text, full: html, text

d05d605337490a39f80d14cb80a69afe5bcad48d Wed Apr 29 17:17:47 2026 -0700

• Releasing the mm10 ENCODE4 cCREs tracks. Removed the alpha,beta tag from encode.cCREs.override.ra and removed the encodeCcreCombined.old.ra include, refs #37131
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 2, context: html, text, full: html, text

b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700

• Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
  • src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html - lines changed 79, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html - lines changed 74, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html - lines changed 76, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html - lines changed 76, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html - lines changed 89, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegDnase.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html - lines changed 58, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html - lines changed 48, context: html, text, full: html, text