ef238e6ab90d807a28fc144fa520b50c0d1b9801 mspeir Mon Nov 3 17:12:17 2025 -0800 changing genome-source to github references, refs #35031 diff --git src/hg/htdocs/goldenPath/help/barChart.html src/hg/htdocs/goldenPath/help/barChart.html index bd4d3074a39..6821bd55d0d 100755 --- src/hg/htdocs/goldenPath/help/barChart.html +++ src/hg/htdocs/goldenPath/help/barChart.html @@ -459,31 +459,31 @@ <p> Also, if you click the "Return to Genome Browser" link, you will see only these selection bars are displayed.</p> <div class="text-center"> <img src="../../images/barChartFacets4.png" alt="Example4 of Facets on barCharts" width="700"> </div> <p> In this image after making the selections browsing ACE2 the "zoom out" button has been clicked to also view nearby genes where the expression of these tissue selections for the gene PIR is quite noticeably different.</p> <h6 id="example7">Example #7</h6> <p> In this example, we will be using command-line tools that were used to create the single-cell tracks available on hg38. For more in-depth examples of these tools, take a look at the following -<a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/makeDb/doc/hg38/gtex.txt#L711" +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/gtex.txt#L711" target="_blank">makedoc</a> for a real-life example. </p> <p> The <code>matrixClusterColumns</code> command converts a single cell gene expression matrix to a cell-type gene expression matrix. It takes a cell-by-cell metadata matrix that refers to the same cells as a gene expression matrix and combines the gene expression values for all cells of a given type into a single value representing the cell type. It can also be used on other metadata fields to produce matrices that show mean or average gene expression levels for a donor, an organ, or any other metadata field or combination of fields. The following command uses the <a href="/goldenPath/help/examples/barChart/singleCell/exprMatrix.tsv">exprMatrix.tsv</a> and <a href="/goldenPath/help/examples/barChart/singleCell/meta.tsv">meta.tsv</a> files to create six files: prepMatrix.tsv, prepStats.tsv, TissueCompMatrix.tsv, TissueCompStats.tsv, SexMatrix.tsv, and SexStats.tsv. </p> <pre>