Single Cell RNA-Seq Data Analysis Workshop

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Single Cell RNA-Seq Data Analysis Workshop

Single Cell RNA-Seq Data Analysis Workshop

By Gladstone Bioinformatics Core

When and where

Date and time

Tuesday, August 20, 2019 · 9am - 5pm PDT


UCSF Mission Bay Campus Mission Hall, 550 16th Street Room 1401/1402 San Francisco, CA 94158

Refund Policy

Refunds up to 7 days before event
Eventbrite's fee is nonrefundable.

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)

About the organizer