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/affyTransfrags.html src/hg/makeDb/trackDb/human/affyTransfrags.html
index 99c62b5b11f..e947f437552 100644
--- src/hg/makeDb/trackDb/human/affyTransfrags.html
+++ src/hg/makeDb/trackDb/human/affyTransfrags.html
@@ -1,20 +1,20 @@
 <H2>Description</H2>
 <P>
 This track represents regions of chromosomes 6, 7, 13,
 14, 19, 20, 21, 22, X, and Y that are thought to be transcribed (transfrags),
-based on the transcriptome data from <A HREF="http://www.affymetrix.com" 
+based on the transcriptome data from <A HREF="https://www.affymetrix.com" 
 TARGET=_blank>Affymetrix</A>. This track is a
 preview of the Phase Two Affymetrix transcriptome project and is based
 on hybridzation of mRNA from the SK-N-AS cell line as seen in the <a
 href="../cgi-bin/hgTrackUi?g=affyTranscription">Transcription</a>
 track. Data from seven additional cell lines will be available when
 the project is completed.  While the coverage of the genome is much
 larger and the probe density greater, the data generation 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>
 Transfrags that have a strong blat hit elsewhere in the genome are
 displayed in a lighter shade of blue. Those that overlap a