Single Cell RNA-Seq Data Analysis Workshop

Gladstone Bioinformatics Core

UCSF Mission Bay Campus

During this one-day hands-on workshop, we will cover techniques, platforms and methods that are used in analyzing single cell data. The workshop has two hands-on sessions: an introductory session in the morning and a more advanced session in the afternoon. The morning session will focus on analysis using Seurat and Monocle. In the afternoon, we will have three advanced hands-on sessions ranging from network analysis of single cell datasets in Cytoscape, normalization and differential analysis outside of Seurat and querying a Single Cell Atlas for cell types. Laptop required.Instructor’s note: Please sign up only for the session that matches your experience level and learning goals. Review the requirements and details below before registering for a session. Basic Session (9am-12pm): Required experience<ul><li>Familiarity with R and RStudio (e.g., reading in files, working with lists and dataframes)</li><li>Some exposure to RNA-seq datasets</li></ul>Part 1: Set-up with breakfast (9-10am)Part 2: Single Cell RNA-seq Analysis with Seurat - David Joy (10am-12pm) A Brief Introduction to Single Cell Data in R (10:00-10:30)<ul><li>Intro to R-markdown notebooks</li><li>Understanding single cell counts data</li><li>Loading counts data into Seurat</li></ul> Single Cell Analysis using Seurat (10:30-11:30)<ul><li>The Seurat normalization and clustering pipeline</li><li>Unbiased cluster analysis</li><li>Assigning cell type identities</li><li>Subsetting and subpopulation analysis</li></ul> Pseudo Time Analysis using Monocle (11:30-12:00)<ul><li>The Monocle normalization and clustering pipeline</li><li>Unbiased trajectory analysis</li><li>Trajectory analysis using experimental annotations</li></ul>Advanced Session (12pm-5pm):Required experience<ul><li>Comfortable with R, RStudio and analytical software</li><li>Prior experience running Seurat and working with single cell data</li><li>Ready for more advanced topics and methods</li></ul>Part 3: Set-up and Q&amp;A with lunch (12 - 2pm)Part 4: Analysis Beyond Seurat (2-5pm) Network analysis of single cell datasets in Cytoscape (2:00-2:45)<ul><li>Introduction to Cytoscape for network visualization</li><li>Introduction to network interaction databases and enrichment analysis</li><li>End-to-end functional characterization of clusters resulting from single cell analysis</li></ul> Normalization and differential expression (2:45-3:45)<ul><li>Short Introduction to Experimental Design, Batch Effects, P-values and Multiple testing</li><li>Normalization of reads for potential batch effects</li><li>Statistically rigorous association of gene expression with variable of interest</li></ul> Querying a Single Cell Atlas for Cell Type (3:45-4:15)<ul><li>Load single cell atlas and counts for the cells to query</li><li>Reformat data to the SingleCellExperiment class</li><li>Create an index for the atlas</li><li>Query the atlas</li><li>Visualize the results</li></ul> Q&amp;A with Instructors (4:15-5:00)

Our {communityGuidelinesLink} describe the sort of content we prohibit on Eventbrite. If you suspect an event may be in violation, you can report it to us so we can investigate.

To report other categories of prohibited or illegal content, submit {link}

Single Cell RNA-Seq Data Analysis Workshop

More events from Gladstone Bioinformatics Core

Discover more events from Gladstone Bioinformatics Core, from Science & Tech to other experiences you might love.

Single Cell RNA-Seq Data Analysis Workshop

More events from Gladstone Bioinformatics Core

Discover more events from Gladstone Bioinformatics Core, from Science & Tech to other experiences you might love.

You might also like...

Browse more events with different dates, prices, and formats to find your next great experience.