Skip to main content

HSLS MolBio Workshops: Single Cell RNA-Seq

Information about hands-on bioinformatics classes

Workshop Objective

This is a 4½ hour workshop on the techniques, platforms, and methods used in analyzing single cell RNA-Seq data (scRNA-Seq). The morning session (10 am - 12 pm) starts with a presentation from the Genomics Research Core on best practices in sample handling, followed by an overview of the basic steps involved in scRNA-Seq data analysis. The afternoon session (1 pm - 3:30 pm) focuses on software demonstration using HSLS-licensed Partek Flow software.

Participants will learn how to

  • import FASTQ files from scRNA-Seq experiments using GEO
  • perform quality checks (QC) on single cell data
  • filter and normalize of data
  • generate PCA and t-SNE plots to visualize data
  • identify cell populations, biomarkers, and differential gene expression
  • perform trajectory analyses

Target Audience:

Experimental biologists seeking to analyze scRNA-Seq data generated through experiments or retrieved from a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.


Please include the following statement in the acknowledgments section for all publications, posters, and presentations -> Data analysis was performed using Partek Flow software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh.

Workshop Evaluation

Key References

The Health Sciences Library System supports the Health Sciences at the University of Pittsburgh.

© 1996 - 2020 Health Sciences Library System, University of Pittsburgh. All rights reserved.
Contact the Webmaster

University of Pittsburgh Libraries