6f0258a40a9faf0ede69fcf5731c83ec3857bb92 lrnassar Fri Apr 3 10:06:26 2026 -0700 Adding newsarch and indexNews entries for new heatmap display mode documentation. refs #36176 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 7fec4879967..84dc1b69b22 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -48,33 +48,78 @@ </div> </div> </div> <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> -<!-- ============= 2025 archived news ============= --> +<!-- ============= 2026 archived news ============= --> + <a name="2026"></a> +<a name="040326"></a> +<h2>Apr. 3, 2026 New heatmap display mode for bigBed tracks</h2> +<p> +We are pleased to announce a new +<a href="/goldenPath/help/heatmap.html" target="_blank"><b>heatmap</b> display +mode</a> for the Genome Browser.</p> +<p> +Heatmaps replace the standard block-and-line gene +display with a color-coded grid: each block position along the item (e.g., an exon) +becomes a column, each row represents a sample or condition, and cells are colored +by score using a customizable gradient. This makes it easy to spot patterns in +multi-sample quantitative data—such as variant effects, gene expression, or +methylation levels—directly in their genomic context. +</p> +<div class="text-center"> + <a href="https://genome.ucsc.edu/s/view/heatmap_example" target="_blank"> + <img src="/images/heatmap_example.png" alt="Heatmap track showing a color-coded grid + of variant effect scores across genomic positions, with rows for each amino acid + substitution and colors ranging from blue (low) through silver to red (high)" + width='90%'></a> +</div> +<p> +The heatmap display is already in use on our +<a href="/cgi-bin/hgTrackUi?db=hg38&g=mavedb_maps" target="_blank">MaveDB Experiment +Heatmaps</a> track, which presents the results of multiplexed assays of variant +effects across gene transcripts. In the example above, each row is an amino acid +substitution and each column is a position along the transcript, with +<span style="color: #FF0000; font-weight: bold;">red</span> cells indicating +higher functional scores and +<span style="color: #0000FF; font-weight: bold;">blue</span> cells indicating lower +scores.</p> +<p> +To create your own heatmap tracks, add +<code>style heatmap</code> to a bigBed track’s trackDb entry along with extra +fields for row labels, color bounds, and score arrays. Our new +<a href="/goldenPath/help/heatmap.html" target="_blank">heatmap documentation page</a> +walks through the entire process step by step, from preparing your data to loading it +in a track hub. +</p> +<p> +For more information on bigBed and other supported data formats, see our +<a href="/FAQ/FAQformat.html" target="_blank">data file formats FAQ</a>. +</p> + <a name="040126"></a> <h2>Apr. 1, 2026 Genome Defense</h2> <p> The Science League desperately needs your assistance to defend the Genome from the forces of the traitorous XRRA1. <a href="../goldenPath/extras/april_1_2026.html">Board your ship and join the battle now!</a> </p> <a name="032826"></a> <h2>Mar. 28, 2026 New UCSC Genome Browser glossary page</h2> <p> Have you ever wondered what we mean by "track" or what the difference is between "haplotype" and "fix" sequences? We are pleased to announce the release of a new <a href="/docs/genomeBrowserGlossary.html" target="_blank">Genome Browser Glossary</a> page. It provides a guide to the