84fff89cc215a064df57b22b843ddece6c0e1739
mspeir
  Thu Jun 20 03:12:17 2019 -0700
Tweaks to cell browser section. Minor white space formatting of Tabula Muris section. refs #22679

diff --git src/hg/htdocs/singlecell.html src/hg/htdocs/singlecell.html
index 2199460..8d6137e 100755
--- src/hg/htdocs/singlecell.html
+++ src/hg/htdocs/singlecell.html
@@ -56,60 +56,71 @@
 <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>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, if you have suggestions, 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>
+        The <a href="https://cells.ucsc.edu" target="_blank">UCSC Cell Browser</a>
+        is a fast, lightweight viewer for single-cell data. You can:
+        <ul>
+          <li>View 2D plots of cells arranged by algorithms such as t-SNE or UMAP</li>
+          <li>Color cells by metadata and gene expression</li>
+          <li>View cluster marker genes and selected dataset-relevant genes</li>
+          <li>View heatmap showing selected gene expression across clusters</li>
+          <li>Rename clusters and add custom annotations to a selected set of cells</li>
+        </ul>
+        Contact us at
+        <a href="mailto:&#99;&#101;&#108;&#108;s&#64;&#117;&#99;s&#99;.
+        &#101;&#100;&#117;">
+        &#99;&#101;&#108;&#108;s&#64;&#117;&#99;s&#99;.
+        &#101;&#100;&#117;</a> to request new datasets or suggest improvements.
+        <!-- above address is cells at ucsc.edu -->
+        To set up your own cell browser, follow our <a href="https://cellbrowser.readthedocs.io/"
+        target="_blank">installation and set up instructions</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.
         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>
+
         <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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