File Changes for lrnassar

v496_preview2 to v496_base (2026-03-23 to 2026-03-30) v496

• src/hg/htdocs/ENCODE/analysis.html
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    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/ENCODE/fileFormats.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/contribTracks.html
  • lines changed 173, context: html, text, full: html, text
    944fa6bbf93daeaac9d5223930696cccccfa5197 Fri Mar 27 17:25:06 2026 -0700
    Updating the page to improve the flow, structure, be clear that the file names need to be identical, and include a new example hub, refs #36957
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 12, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/goldenPath/help/hubQuickStartFilter.html
  • lines changed 18, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
  • lines changed 4, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 3, context: html, text, full: html, text
    6f00f33a31c1cec74f33b7e408165005f8b87e37 Wed Mar 25 13:45:08 2026 -0700
    Fix inaccurate alt text in sessions.html per QA feedback. refs #37254 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 16, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
  • lines changed 10, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/staff.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/makeDb/doc/hg38/encode4.regulation.txt
  • lines changed 249, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 79, context: html, text, full: html, text
    7e9cf9d7dace5cd9a0519bee134364b87b86d832 Fri Mar 27 12:01:25 2026 -0700
    Updating makedocs for hg38 and mm10 ENCODE4 Regulation tracks to reflect all changes from 2026-03-27: priorities, symlink renaming, color darkening, colorSettingsUrl, longLabel cleanup, Data Access sections, HTML audit fixes, code review fixes, and local ENCFF file cleanup (4.3 TB freed). refs #34923
• src/hg/makeDb/doc/mm10.encode4.regulation.txt
  • lines changed 208, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 76, context: html, text, full: html, text
    7e9cf9d7dace5cd9a0519bee134364b87b86d832 Fri Mar 27 12:01:25 2026 -0700
    Updating makedocs for hg38 and mm10 ENCODE4 Regulation tracks to reflect all changes from 2026-03-27: priorities, symlink renaming, color darkening, colorSettingsUrl, longLabel cleanup, Data Access sections, HTML audit fixes, code review fixes, and local ENCFF file cleanup (4.3 TB freed). refs #34923
• src/hg/makeDb/scripts/encode4regulation/convert_to_bigcomposite.py
  • lines changed 427, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/encode4regulation/generate_composites.py
  • lines changed 438, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/encode4regulation/generate_multiwig_ra.py
  • lines changed 269, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/encode4regulation/validate_encode_urls.py
  • lines changed 268, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
  • lines changed 1, context: html, text, full: html, text
    95860982a496454aec2aab3df0e6cb2c4b7760b4 Thu Mar 26 17:47:15 2026 -0700
    Adjusting track priorities in regulation group for hg38 and mm10. hg38: cCREs 0.8, wgEncodeReg4 0.9, wgEncodeReg 1. mm10: cCREs 0.4, encode4Reg 0.5, tabulaMuris 1. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.alpha.ra
  • lines changed 407, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html
  • lines changed 148, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 10, context: html, text, full: html, text
    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra
  • lines changed 3327, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    95860982a496454aec2aab3df0e6cb2c4b7760b4 Thu Mar 26 17:47:15 2026 -0700
    Adjusting track priorities in regulation group for hg38 and mm10. hg38: cCREs 0.8, wgEncodeReg4 0.9, wgEncodeReg 1. mm10: cCREs 0.4, encode4Reg 0.5, tabulaMuris 1. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 209, context: html, text, full: html, text
    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html
  • lines changed 84, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 38, context: html, text, full: html, text
    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 19, context: html, text, full: html, text
    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html
  • lines changed 83, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 53, context: html, text, full: html, text
    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 19, context: html, text, full: html, text
    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    7c4f2e656763f789dafcabae4c2c82f5b581d43f Fri Mar 27 10:15:45 2026 -0700
    Replacing underscores with spaces in all 6,747 hg38 bigComposite subtrack longLabels for readability. Converts e.g. "Homo_sapiens_K562_stably_expressing" to "Homo sapiens K562 stably expressing". mm10 labels were already correct. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    7c4f2e656763f789dafcabae4c2c82f5b581d43f Fri Mar 27 10:15:45 2026 -0700
    Replacing underscores with spaces in all 6,747 hg38 bigComposite subtrack longLabels for readability. Converts e.g. "Homo_sapiens_K562_stably_expressing" to "Homo sapiens K562 stably expressing". mm10 labels were already correct. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    7c4f2e656763f789dafcabae4c2c82f5b581d43f Fri Mar 27 10:15:45 2026 -0700
    Replacing underscores with spaces in all 6,747 hg38 bigComposite subtrack longLabels for readability. Converts e.g. "Homo_sapiens_K562_stably_expressing" to "Homo sapiens K562 stably expressing". mm10 labels were already correct. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra
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    95860982a496454aec2aab3df0e6cb2c4b7760b4 Thu Mar 26 17:47:15 2026 -0700
    Adjusting track priorities in regulation group for hg38 and mm10. hg38: cCREs 0.8, wgEncodeReg4 0.9, wgEncodeReg 1. mm10: cCREs 0.4, encode4Reg 0.5, tabulaMuris 1. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    95860982a496454aec2aab3df0e6cb2c4b7760b4 Thu Mar 26 17:47:15 2026 -0700
    Adjusting track priorities in regulation group for hg38 and mm10. hg38: cCREs 0.8, wgEncodeReg4 0.9, wgEncodeReg 1. mm10: cCREs 0.4, encode4Reg 0.5, tabulaMuris 1. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegDnase.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra
  • lines changed 3353, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html
  • lines changed 81, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 23, context: html, text, full: html, text
    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 19, context: html, text, full: html, text
    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.alpha.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
  • lines changed 3, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 11, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/utils/qa/buildPublicSessionThumbnailsIndexPage.py
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    c2d63f068433c6f321c57b380733ace4bbec12b7 Thu Mar 26 13:21:13 2026 -0700
    Fix UnboundLocalError in buildPublicSessionThumbnailsIndexPage.py when sessions have unusual names that cause the trash line parsing to fail. Skip sessions where sessionUrl was not set instead of crashing. No RM. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/utils/qa/mlqAutomate.py
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    bc70099d05e549ea2cd85689d7eaeac3d62bef3e Fri Mar 27 15:05:41 2026 -0700
    Fix mlqAutomate quote stripping for Apple Mail/Outlook Mac format. refs #37297 The From:/Date:/To: multi-line quote header used by Apple Mail and Outlook for Mac was not being detected, only From:/Sent:/To: (Windows Outlook). This caused quoted thread history to remain in the email body, triggering false-positive duplicate detection and skipping legitimate new replies.