src/hg/htdocs/singlecell.html 602a1b57a8de2305f98b3cc8a84650fd11fcc45d

602a1b57a8de2305f98b3cc8a84650fd11fcc45d
max
  Tue May 14 05:32:00 2019 -0700
changes to singlecell page, refs #22679

diff --git src/hg/htdocs/singlecell.html src/hg/htdocs/singlecell.html
index bc04904..f1bd996 100755
--- src/hg/htdocs/singlecell.html
+++ src/hg/htdocs/singlecell.html
@@ -1,107 +1,112 @@
 <!DOCTYPE html>
-<!--#set var="TITLE" value="GTEx Resources at UCSC" -->
+<!--#set var="TITLE" value="Single cell resources at UCSC" -->
 <!--#set var="ROOT" value="." -->
 
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 </style>
 
 <h1>Single cell resources at UCSC</h1>
 <p>
 Single cell experiments measure thousands of gene loci in thousands of cells at
 the same time. It is challenging explore and share these high-dimensional data.
 The UCSC Genome Browser is adding published datasets as tracks and a new
 visualisation tool:
 </p>
 <p>
 <dl>
 <dt><a target="_blank" 
     href="https://cells.ucsc.edu">
             UCSC Cell Browser</a></dt>
     <dd>Interactively color dimensionality reduction plots by cell annotation or genes</dd>
 <dt><a target="_blank" 
     href="../cgi-bin/hgTrackUi?db=mm10&g=tabulaMuris">
             Tabula Muris</a></dt>
-    <dd>A Genome Browser track showing single cell RNA-seq gene expression, genome coverage and splice sites</dd>
+    <dd>Genome Browser track showing single cell RNA-seq gene expression, genome coverage and splice sites</dd>
 </dl>
 
 <div class="row">
     <div class="col-md-6">
         <h2>UCSC Cell Browser</h2>
         <p>With the <a target=_blank href="https://cells.ucsc.edu">Cell Browser</a>
         you can plot cells arranged by algorithms like t-SNE or UMAP. Color
         these by annotated meta data or genes via the left side bar.  Select
         cells via the legend on the right or with the rectangle selection tool.
         You can export the current cell selection or annotate it via the "Tools" menu.
+        We are happy to add your favorite dataset, contact us at
+        <a href="mailto:cells@ucsc.edu">cells@ucsc.edu</a>.
+        To set up your own cell browser, follow the instructions at 
+        <a href="https://cellbrowser.rtfd.org">cellbrowser.readthedocs.org</a>.
         </p>
+
         <p class="text-center">
         <a target=_blank href="https://cells.ucsc.edu" alt="Screenshot of UCSC Cell Browser">
             <img style="width:100%" src="<!--#echo var="ROOT" -->/images/cellbrowser.png">
         </a>
         </p>
     </div>
     <div class="col-md-6">
         <h2>Single cell datasets in the UCSC Genome Browser</h2>
         <p>
 Below is a screenshot of a  
 <a target="_blank" 
 href="http://genome.ucsc.edu/s/Max/tabMuris">public session</a>
-that highlights the Tabula Muris gene expression track
+that highlights the Tabula Muris gene expression track.
 The session shows the Sox10 locus. The gene expression track at the top shows that the
 gene is only well expressed in basal cells (orange), mammary gland (blue) and oligodendrocytes (pink).
 These cell type names are shown when you hover with the mouse over the bars on
 the genome browser. The coverage tracks below show that all exons are
 transcribed in these, but the last exon is also transcribed in stromal cells
 and some non-coding transcription is seen in goblet cells 3' of the gene. The
 splicing tracks below show that proper splicing is limited to the four cell types
 described above. This is also a non-coding region conserved in zebrafish and chicken.
     <p class="text-center">
     <a target="_blank" href="http://genome.ucsc.edu/s/Max/tabMuris" alt="genome browser session link">
             <img src="../images/screenshot-tabMuris.png" style='width:100%'>
     </a>
     </p>
     </div>
 </div>
 
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