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/affyTranscriptome.html src/hg/makeDb/trackDb/affyTranscriptome.html
index a83c1746beb..52b00ee3c92 100644
--- src/hg/makeDb/trackDb/affyTranscriptome.html
+++ src/hg/makeDb/trackDb/affyTranscriptome.html
@@ -1,19 +1,19 @@
 <H2>Description</H2>
 <P>
 Transcriptome data for chromosomes 21 and 22 from <a
-href="http://www.affymetrix.com">Affymetrix</a>, as described in 
+href="https://www.affymetrix.com">Affymetrix</a>, as described in 
 P. Kapranov et al. 
 <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>, 296(5569):916-9).
 In general, the data presented
 is the perfect match - mis-match value. Different experiments were
 normalized by setting the average value to be the same for each
 chip. Replicates for different cell types were averaged together to
 produce the data seen in "full" mode for each cell type. In dense
 mode, or at the top of the track in full mode, &quot;Transcriptome&quot; displays
 the maximum value over all experiments for that probe, the idea being
 to paint as many transcribed regions as possible. 
 <P>
 To present a more
 interpretable display when zoomed out, averages have been precalculated