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Single Cell RNA-Seq Data Analysis Workshop
Single Cell RNA-Seq Data Analysis Workshop
When and where
Date and time
Tuesday, August 20, 2019 · 9am - 5pm PDT
Location
UCSF Mission Bay Campus Mission Hall, 550 16th Street Room 1401/1402 San Francisco, CA 94158
Refund Policy
About this event
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
- Familiarity with R and RStudio (e.g., reading in files, working with lists and dataframes)
- Some exposure to RNA-seq datasets
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)
- Intro to R-markdown notebooks
- Understanding single cell counts data
- Loading counts data into Seurat
Single Cell Analysis using Seurat (10:30-11:30)
- The Seurat normalization and clustering pipeline
- Unbiased cluster analysis
- Assigning cell type identities
- Subsetting and subpopulation analysis
Pseudo Time Analysis using Monocle (11:30-12:00)
- The Monocle normalization and clustering pipeline
- Unbiased trajectory analysis
- Trajectory analysis using experimental annotations
Advanced Session (12pm-5pm):
Required experience
- Comfortable with R, RStudio and analytical software
- Prior experience running Seurat and working with single cell data
- Ready for more advanced topics and methods
Part 3: Set-up and Q&A with lunch (12 - 2pm)
Part 4: Analysis Beyond Seurat (2-5pm)
Network analysis of single cell datasets in Cytoscape (2:00-2:45)
- Introduction to Cytoscape for network visualization
- Introduction to network interaction databases and enrichment analysis
- End-to-end functional characterization of clusters resulting from single cell analysis
Normalization and differential expression (2:45-3:45)
- Short Introduction to Experimental Design, Batch Effects, P-values and Multiple testing
- Normalization of reads for potential batch effects
- Statistically rigorous association of gene expression with variable of interest
Querying a Single Cell Atlas for Cell Type (3:45-4:15)
- Load single cell atlas and counts for the cells to query
- Reformat data to the SingleCellExperiment class
- Create an index for the atlas
- Query the atlas
- Visualize the results
Q&A with Instructors (4:15-5:00)