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, "Transcriptome" 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