198c9b8daecc44fbda6a6494c566c723920f030a
lrnassar
  Wed Mar 11 18:25:21 2026 -0700
Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.

diff --git src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html
index 80d4c78d4fd..2bf5b3b6e24 100644
--- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html
+++ src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html
@@ -1,105 +1,105 @@
 <h2>Description</h2>
 <p>
 These tracks contain information relevant to the regulation of transcription from the
 <a href="/ENCODE/" target="_blank">ENCODE Project</a>.
 
 <ul>
   <li>The <i>TF rPeak Clusters</i> track shows genomic regions bound by DNA-associated proteins 
 involved in transcriptional regulation from ENCODE 4.</li>
   <li>The <i>Transcription</i> track shows transcription
 levels assayed by sequencing of polyadenylated RNA from a variety of cell types.</li>
   <li>The <i>Layered H3K4Me1</i> and <i>Layered H3K27Ac</i> tracks show where modification of histone proteins
 is suggestive of enhancer and, to a lesser extent, other regulatory activity.  These histone 
 modifications, particularly H3K4Me1, are quite broad.  The actual enhancers are typically just a 
 small portion of the area marked by these histone modifications.</li>
   <li>The <i>Layered H3K4Me3</i> 
 track shows a histone mark associated with promoters.</li>
   <li>The <i>DNase I Hypersensitivity</i> tracks indicate
 where chromatin is hypersensitive to cutting by the DNase enzyme, which has 
 been assayed in a large number of cell types. Regulatory regions, in general, tend to be 
 DNase-sensitive, and promoters are particularly DNase-sensitive.</li>
   <li>The <i>Txn Factor ChIP</i>
 tracks show DNA regions where transcription factors, proteins responsible for 
 modulating gene transcription, bind as assayed by chromatin immunoprecipitation with antibodies 
 specific to the transcription factor followed by sequencing of the precipitated DNA (ChIP-seq).</li>
 </ul>
 </p>
 
 <p>
 These tracks complement each other and together can shed much light on regulatory DNA. The histone
 marks are informative at a high level, but they have a resolution of just ~200 bases and do not
 provide much in the way of functional detail.  The DNase hypersensitivity assay is higher in
 resolution at the DNA level and can be done on a large number of cell types since it's just 
 a single assay. At the functional level, DNase hypersensitivity suggests that a 
 region is very likely to be regulatory in nature, but provides little information beyond that.
 The transcription factor ChIP assay has a high resolution at the DNA level and, due to the very
 specific nature of the transcription factors, is often informative with respect to functional
 detail.  However, since each transcription factor must be assayed separately, the information is
 only available for a limited number of transcription factors on a limited number of cell lines. 
 Though each assay has its strengths and weaknesses, the fact that all of these assays are 
 relatively independent of each other gives increased confidence when multiple tracks are 
 suggesting a regulatory function for a region.
 </p>
 
 <p>
 For additional information, please click on the hyperlinks for the individual tracks above.
 Also note that additional histone marks and transcription information is available in other
 ENCODE tracks.  This integrative supertrack just shows a selection of the most informative data of
 most general interest.
 </p>
 
 <h2>Display Conventions</h2>
 <p>
 By default, the transcription and histone mark displays use a transparent overlay method of 
 displaying data from a number of cell lines in a single track.  Each of the cell lines in this track
 is associated with a particular color, and these colors are relatively light and saturated so
 as to work best with the transparent overlay. The color of the transcription and histone mark tracks
 match their versions from their lifted source on the hg19 assembly.</p>
 <p>
 The DNase tracks, which were not lifted from hg19, are colored differently 
 to reflect similarity of cell types. There are three DNase tracks starting with a transparent
 overlay DNase Signal Track to allow viewing signals from all 95 cell types in one track.
 The individual signals and the same coloring scheme can also be found in the DNase HS Track
 where processed peaks and hotspots are also called out as gray boxes with the darkness of
 each box reflecting the underlying signal value. Lastly, in the DNase Clusters track all observed
 hypersensitive regions in the different cell lines at the same location were clustered into a single box
 where a number to the left of the box indicates how many cell types showed a hypersensitivity 
-region and the darkness of the grey box is proportional to the the maximum value seen from one of
+region and the darkness of the grey box is proportional to the maximum value seen from one of
 the underlying cell lines. Clicking on these item takes you to a details page where
 additional information displays, such as the list of cell types that combined to form
 the cluster in the DNase Clusters track.
 </p>
 
 <h2>Data Access</h2>
 <p>
 The raw data for ENCODE 3 Regulation tracks can be accessed from 
 <a href="hgTables?db=hg38">
 Table Browser</a> or combined with other data-sets through <a href="hgIntegrator">
 Data Integrator</a>. For automated analysis and downloads, the track data files can be downloaded 
 from our <a href="https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/">downloads server</a> or queried
 using the <a href="../../goldenPath/help/api.html">JSON API</a> or the 
 <a href="../../goldenPath/help/mysql.html">Public SQL</a> Individual regions or the whole genome 
 annotation can be accessed as text using our utility bigBedToBed. Instructions for downloading 
 the utility can be found 
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. That 
 utility can also be used to obtain features within a given range, e.g. 
 <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/wgEncodeRegDnase/wgEncodeRegDnaseUwA549Hotspot.broadPeak.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt></p>
 <p>
 For sorting transcription factor binding sites by cell type, we recommend you use the following
 download 
 <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/encRegTfbsClustered/">file for hg38</a>.
 </p>
 
 
 <H2>Credits</H2>
 <p>
 Specific labs and contributors for these datasets are listed in the Credits section 
 of the individual tracks in this super-track. The integrative view presented here was developed by Jim Kent at UCSC.</P>
 
 <H2> Data Use Policy </H2>
 <P> <B>Users may freely download, analyze and publish results based on any ENCODE data without 
 restrictions.</B>
 Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. </p>
 <B><I>Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE
 production laboratory(s) that generated the datasets used, as described in
 <A target="_blank" href="https://www.encodeproject.org/help/citing-encode/">Citing ENCODE</A>.</B></I></p>