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 @@ -1,80 +1,80 @@ --- title: "UCSC Genome Browser Slide Decks" --- This page collects training slides for the UCSC Genome Browser. Each slide deck has been curated with a specific purpose, from basic navigation to interpreting clinical variants. They are self-contained web decks: open one in any browser, present it full-screen (press <kbd>F</kbd>), read the presenter notes (press <kbd>S</kbd>, which opens them in a separate browser tab; close that tab when you are done with them), or jump to any slide from its **Contents** page. Feel free to use them in your courses or local trainings. [Contact us](/contacts.html) to suggest new slide decks or improvements to the current ones. ## Deck 1: UCSC Genome Browser Basics 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. **[▶ Open the deck](/docs/slideDecks/tutorial3-clinical/presentation/)** · [Contents](/docs/slideDecks/tutorial3-clinical/tableOfContents/) <br> <iframe src="/docs/slideDecks/tutorial3-clinical/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 3: Clinical Examples and Variant Interpretation"></iframe> ## Deck 4: Clinical Case Studies A set of real diagnostic cases spanning variant classes, each opening as a live Genome Browser session: coding variants, splicing (deep-intronic and synonymous), non-coding and regulatory variants, structural variants (CNVs), and repeat expansions. **[▶ Open the deck](/docs/slideDecks/tutorial4-clinical-cases/presentation/)** · [Contents](/docs/slideDecks/tutorial4-clinical-cases/tableOfContents/) <br> <iframe src="/docs/slideDecks/tutorial4-clinical-cases/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 4: Clinical Case Studies"></iframe> ## Deck 5: Teaching with the Browser Ready-made, interactive teaching modules from our [Education portal](/training/education/): the central dogma (reading frames, codons, splicing), variant effects (synonymous, missense, nonsense, frameshift), and real disease and evolution case studies. Each module is a clickable session plus a short description of that session and what it shows, ready to drop into a lecture or assignment. **[▶ Open the deck](/docs/slideDecks/tutorial5-teaching/presentation/)** · [Contents](/docs/slideDecks/tutorial5-teaching/tableOfContents/) <br> <iframe src="/docs/slideDecks/tutorial5-teaching/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 5: Teaching with the Browser"></iframe>