CCMI - Workshop

Single-cell Analysis with the GenePattern Notebook Environment


Michael Reich, Asst. Director of Bioinformatics, UC San Diego

Ted Liefeld, Chief Software Architect, UC San Diego

Edwin Juarez, Bioinformatics Scientist, UC San Diego

Alex Wenzel, Bioinformatics and Systems Biology Graduate Student, UC San Diego

GenePattern ( enables researchers at all levels of computational expertise to use hundreds of tools for the analysis of gene expression including single cell RNA-seq analyses, sequence variation, proteomics and more, all through an intuitive Web-based interface.

The GenePattern Notebook environment ( integrates GenePattern with the popular Jupyter Notebook system to allow users to incorporate compute-intensive genomic analyses into accessible notebooks without the need to program.  

In the short time that single-cell RNA-seq technology has been available, it has produced unprecedented insights into the function and regulation of tissues and promises a revolution in our understanding of the mechanisms of disease. In this workshop, participants will learn the GenePattern Notebook environment and will use it to analyze single-cell RNA-seq data using the popular Seurat and Conos packages. 


  • GenePattern and Jupyter Notebook essentials
  • Importing Human Cell Atlas data into GenePattern
  • Single-cell RNA-seq clustering with Seurat
    • Preprocessing
    • Clustering
    • Visualizing cluster markers
  • Wiring together multiple single-cell experiments with Conos
    • Preprocessing multiple cohorts
    • Aligning datasets with joint graphs
    • Interpreting clustering results


The only prerequisite is a laptop with a current updated browser (Chrome or Firefox), and basic familiarity with genomic data. Programming experience is NOT required.


  • 9:00 AM Introduction to GenePattern
  • 9:20 AM Jupyter Notebook essentials
  • 9:40 AM GenePattern Notebook features
  • 10:00 AM Single-cell analysis with Seurat
  • 10:30 AM Break
  • 10:45 AM Single-cell analysis with Seurat, ctd.
  • 11:30 AM Single-cell analysis with Conos
  • 12:00 PM Lunch
  • 1:00 PM Class Project
  • 2:00 PM Break
  • 2:15 PM Importing your data into GenePattern Notebook
  • 2:30 PM Open time: bring your own data

Light refreshments and box lunch provided

No Show Policy

 While we do not charge a fee to attend this event, these programs would not be sustainable and available to all wanting to attend, unless all registrants abide by the 48 hour cancellation notice policy. A no-show will also limit your ability to book our events in the future. Thank you in advance for your cooperation.  


A map of the Skaggs Pharmaceutical Sciences Building (PSB) can be viewed HERE. The closest parking lots include the Osler Parking Structure, P602, P603 and the Gilman Parking structure. Hourly rates are posted at meters; cards are accepted. Additionally, Valet Parking is available in lot P610 on Osler Lane. If using the UC San Diego Shuttle, exit at Gilman Drive and Meyers Lane, then walk south towards School of Medicine.   

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