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/affy.html src/hg/makeDb/trackDb/affy.html
index 6a16c2098cb..9cad9beeb9a 100644
--- src/hg/makeDb/trackDb/affy.html
+++ src/hg/makeDb/trackDb/affy.html
@@ -1,15 +1,15 @@
 <h2>GNF Gene Expression Atlas Experiments using Affymetrix GeneChips</h2>
 
 <p>A series of experiments using different normal tissues using <a
-href="http://www.affymetrix.com">Affymetrix</a> GeneChips performed
+href="https://www.affymetrix.com">Affymetrix</a> GeneChips performed
 by <a href="http://www.gnf.org">GNF (The Genomics Institute of the
 Novartis Research Foundation) </a>. Alignments displayed on the
 track correspond to the target sequences used by Affymetrix from
 which to choose probes. Color denotes signal intensity on a
 log base 2 scale with darker colors corresponding to lower signal and
 lighter colors corresponding to higher signal. Please note that this
 track is under construction and will not be official until the GNF
 publishes their results.
 
 <p>Track options include the ability to group results by chip type,
 tissue average, and individual chip identification numbers.