089c09e98db52e92da694ab1a0c8891c1a7fd3e8
gperez2
  Thu Apr 2 15:50:07 2026 -0700
Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run).

Updated 261 trackDb HTML and .ra files:
- Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs,
chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations;
removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download,
oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs).
- Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com,
drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains
(blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix);
removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com).
- Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org,
cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org,
hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path).

No RM.

diff --git src/hg/makeDb/trackDb/human/affyTranscription.html src/hg/makeDb/trackDb/human/affyTranscription.html
index c8c3d6f2f15..8fc79448d9f 100644
--- src/hg/makeDb/trackDb/human/affyTranscription.html
+++ src/hg/makeDb/trackDb/human/affyTranscription.html
@@ -1,19 +1,19 @@
 <H2>Description</H2>
 <P>
 This track displays transcriptome data from tiling GeneChips produced by 
-<A HREF="http://www.affymetrix.com" TARGET=_blank>Affymetrix</A>. For the ten
+<A HREF="https://www.affymetrix.com" TARGET=_blank>Affymetrix</A>. For the ten
 chromosomes 6, 7, 13, 14, 19, 20, 21, 22, X, and Y, more than 74 million
 probes were tiled every 5 bp in non-repeat-masked areas 
 and hybridized to mRNA from the SK-N-AS cell line. These data
 are a preview of Phase Two of the transcriptome project, which will
 include data from seven additional cell lines when completed. While the
 coverage of the genome is much larger and the probe density greater,
 the general method is similar to the Phase One project carried out on
 chromosomes 21 and 22  (Kapranov, P. <em>et al</em>. 
 <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11988577" 
 TARGET=_blank>Large-scale transcriptional activity in chromosomes 21 and 
 22.</A> <em>Science</em> <B>296</B>(5569), 916-9 (2002)).</P>
 <P>
 The track is colored blue in areas that are thought to be
 transcribed at a statistically significant level as described in the
 accompanying <a