29d8156c530a7b28618003d89a090c99af49751e brianlee Wed Jun 1 15:58:31 2016 -0700 Adding news release announcement for density graph refs #952 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 60dbb9f..6ff8de3 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -25,30 +25,56 @@ <TR><TH HEIGHT=3></TH></TR> <TR><TD WIDTH=10></TD> <TD> <P> To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the <A HREF="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en" TARGET=_blank>genome-announce</A> mailing list. Please see our <a href="http://genome.ucsc.edu/blog" target=_blank>blog</a> for posts about Genome Browser tools, features, projects and more. </p> <hr> <!-- start news --> + <font color="#006666" size="4"><b>1 June 2016 - New Density Graph Feature!</b></font> + <p> + The Genome Browser is proud to announce a new "density graph" feature for + a variety of tracks, including BAM custom tracks, that converts data into a summary display.</p> + <p> + The density graph feature enables certain track types to be displayed as a bar graph where + the height is proportional to the number of reads mapped to each genomic position. + Through dynamic calculation of items in the current window, this feature plots a line + similar to a wiggle graph that can be customized with a number of + <a href="goldenPath/help/hgWiggleTrackHelp.html" + target="_blank">graph-based configuration options</a> such as drawing indicator lines, + smoothing plots, adjusting graph height and vertical range, and switching from bars to + points. Please note that the feature is best displayed with Display mode set to full + and that the default is auto-Scale data to view. Please note that using this + feature on a <a href="goldenPath/help/gbib.html#GbibMirroring" + target="_blank">virtual machine Genome Browser in a Box (GBiB)</a> may benefit from + increasing memory.</p> + <p> + To turn on the feature click into the track controls for certain track types, + such as a BAM custom track, and check the box next to "Display data as a + density graph" to see graph configurations and then click "Submit". + To see the new density graph feature in use, please see this example + <a href="cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.densityGraph&hgct_customText=track%20type=bam%20name=bamExample%20visibility=full%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam%20doWiggle=1" + target="_blank">session</a>. + <hr> + <font color="#006666" size="4"><b>10 May 2016 - New Gateway Page!</b></font> <p> The UCSC Genome Browser team is proud to announce a newly redesigned <a href="../cgi-bin/hgGateway" target="_blank">Genome Browser Gateway</a> page. The Gateway retains its original functionality as a central access point for all genome assemblies available on our site, while sporting several helpful new features and updates:</p> <ul> <li>Autocomplete searching for any genome browser, genome version, or public hub</li> <li>Species browsing through a scrollable visual "tree" menu based on phylogenetic order</li> <li>Quick access shortcuts to popular browsers</li> <li>New style and color scheme</li> </ul> <p> Please see our <a href="https://youtu.be/5zc9sqd4SD4" @@ -68,44 +94,38 @@ <ul> <li>Browser reset: Genome Browser > Reset All User Settings</li> <li>Track search: Genome Browser > Track Search</li> <li>Add custom tracks: My Data > Custom Tracks</li> <li>Track hubs: My Data > Track Hubs</li> <li>Configure tracks and display: Genome Browser > Configure</li> </ul> <p> We would like to acknowledge the following people for their contributions to the new Gateway: original art by Jeff West Design, concept by Robert Kuhn, software design by Angie Hinrichs, and quality assurance by Cath Tyner.</p> <hr> <!-- start archives --> <!--staged for future release + <font color="#006666" size="4"><b>1 June 2016 - New Density Graph Feature!</b></font> + The Genome Browser is proud to announce a new "density graph" feature for + a variety of tracks, including BAM custom tracks, that converts data into a summary display.</p> + <a href="goldenPath/newsarch.html#060116">Read more</a>. <p> <font color="#006666" size="4"><b>10 May 2016 - New Gateway Page!</b>: </font> The UCSC Genome Browser team is proud to announce a newly redesigned <a href="../../cgi-bin/hgGateway" target="_blank">Genome Browser Gateway page</a>. Please see our <a href="https://youtu.be/5zc9sqd4SD4" target="_blank">Gateway video</a> for an introduction to these new features. <a href="goldenPath/newsarch.html#051016">Read more</a>. --> <p> <font color="#006666" size="4"><b>22 Apr 2016 - Data from the Lens PatSeq Database Now Available</b>: </font> We are pleased to announce the release of a set of tracks containing data from the <a href="https://www.lens.org/" target="_blank">Lens</a> PatSeq database in the UCSC Genome Browser. <a href="goldenPath/newsarch.html#042216">Read more</a>. - - <p> - <font color="#006666" size="4"><b>19 April 2016 - - New Genotyping Tissue Expression Track for hg19 and hg38!</b>: </font> - We are excited to announce the release of a new track based on data from the - <a href="http://commonfund.nih.gov/GTEx/index" - TARGET = _BLANK>Genotyping Tissue Expression Consortium</a> V6 data freeze. - <a href="goldenPath/newsarch.html#042016">Read more</a>. - - </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>