b120644088d912f130ada387e34067b40616edc0 mspeir Mon Jul 27 08:19:30 2026 -0700 minor fixes based on CR, refs #37874 diff --git docs/browserSlideDecks.md docs/browserSlideDecks.md index b06031c4b94..a30d166f323 100644 --- docs/browserSlideDecks.md +++ docs/browserSlideDecks.md @@ -17,31 +17,31 @@ Basic features and navigation of the [main genome browser display](/cgi-bin/hgTracks): configuring tracks and display modes, reading the gene model, browsing the track groups, viewing and extracting DNA, querying the Table Browser, aligning sequences with BLAT, and loading your own data as custom tracks, track hubs, and sessions. **[▶ Open the deck](/docs/slideDecks/tutorial1-basics/presentation/)** · [Contents](/docs/slideDecks/tutorial1-basics/tableOfContents/) <br> <iframe src="/docs/slideDecks/tutorial1-basics/presentation/" width="720" height="450" style="max-width:100%;border:1px solid #ccc;border-radius:6px;" frameborder="0" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true" title="Deck 1: UCSC Genome Browser Basics"></iframe> ## Deck 2: Cancer Data in the Genome Browser An overview of the cancer and clinical databases hosted by the Genome Browser, -organized by **somatic** and **germline** diagnosis CIViC, COSMIC, ClinVar, and TCGA +organized by **somatic** and **germline** diagnosis: CIViC, COSMIC, ClinVar, and TCGA Pan-Cancer for somatic variants, and GenCC, OMIM, and gnomAD for germline questions. These databases are explored with a consistent <em>BRAF</em> V600E example throughout. **[▶ Open the deck](/docs/slideDecks/tutorial2-cancer/presentation/)** · [Contents](/docs/slideDecks/tutorial2-cancer/tableOfContents/) <br> <iframe src="/docs/slideDecks/tutorial2-cancer/presentation/" width="720" height="450" style="max-width:100%;border:1px solid #ccc;border-radius:6px;" frameborder="0" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true" title="Deck 2: Cancer Data in the Genome Browser"></iframe> ## Deck 3: Clinical Examples & Variant Interpretation How to interpret a variant end to end: the **Recommended Track Sets**, the regulatory and epigenetic context that non-coding variants need, worked germline (<em>BRCA2</em>) and somatic (<em>BRAF</em> V600E) examples, expression, and AI predictors such as AlphaMissense and SpliceAI.