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/TFrPeakClusters.html src/hg/makeDb/trackDb/human/TFrPeakClusters.html index dece5049c4f..32b0f53e0d1 100644 --- src/hg/makeDb/trackDb/human/TFrPeakClusters.html +++ src/hg/makeDb/trackDb/human/TFrPeakClusters.html @@ -27,31 +27,31 @@ and the total number of biosamples assayed for the protein. Links to relevant ENCODE ChIP-seq experiments and overlapping ENCODE candidate cis-regulatory elements (cCREs) are also provided.</p> <p>By default, rPeaks for all 912 DNA-associated proteins with ENCODE ChIP-seq data are displayed. Users can customize the display by selecting specific DNA-associated proteins in the track settings.</p> <h2>Methods</h2> <p>2,509 ENCODE ChIP-seq experiments were integrated from 912 DNA-associated proteins across 1,152 unique biosamples to produce representative peaks (rPeaks) for each protein. The processing steps were as follows:</p> <ol> -<li>ChIP-seq peaks for each protein were downloaded from the <a target="_blank" href="http://encodeproject.org">ENCODE Portal</a>, +<li>ChIP-seq peaks for each protein were downloaded from the <a target="_blank" href="https://www.encodeproject.org">ENCODE Portal</a>, generated using the <a target="_blank" href="https://www.encodeproject.org/chip-seq/transcription_factor/"> ENCODE Transcription Factor ChIP-seq Processing Pipeline</a>.</li> <li>Using bedtools merge, ChIP-seq peaks were clustered from the protein’s experiments across all biosamples.</li> <li>In each cluster, the peak with the highest ChIP signal (normalized by sequencing depth) was selected as the rPeak.</li> <li>All ChIP-seq peaks overlapping this rPeak by at least one nucleotide were marked as represented and removed from subsequent clustering rounds.</li> <li>Steps 2-4 were repeated until a final list of non-overlapping rPeaks was generated, representing all ChIP-seq peaks for the protein.</li> </ol> <h2>Data Access</h2> <p>The raw data for the ENCODE TF rPeak track will soon be available.</p> <p> The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>, for download, intersection or correlations with other tracks. To join this track with others