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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.


This workshop is focused on multiomics data analysis - Spatial Transcriptomics. While CITE Seq enables researchers to capture both RNA and surface protein expression simultaneously, the Spatial Transcriptomics method allows researchers to measure mRNA expression in the spatial context of a tissue.

Participants will learn how to

  • import 10x Genomics Spatial Transcriptomics (Visium) data to PartekFlow
  • merge expression data with histological information
  • filter and normalize the data
  • generate UMAP plots to visualize data
  • identify cell populations and biomarkers and compute differential gene expressions between two cell populations

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.

Workshop Materials

Software Registration

Data Download (10x Genomics)

Databases and Tools



  • Cell Ranger and Space Ranger - a set of 10x genomics analysis pipelines that process chromium or visium data
  • Azimuth - a tool for rapid mapping of query datasets to references
  • Garnett - a tool for automated cell type classification



Please include the following statement in the acknowledgments section for all publications, posters, and presentations:

[software name, such as CLC Genomics workbench, Partek Flow ] software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh (RRID:SCR_011975) was used for data analysis.