Workshop Description (Intermediate Course)

This workshop aims to introduce the basic concepts and algorithms for single-cell RNA-seq analysis. It will help participants obtain a better idea of how to use scRNA-seq technology, from considerations in experimental design to data analysis and interpretation. This workshop can serve researchers who are interested in designing an scRNA-seq study or who have acquired scRNA-seq data and would like to learn about different analytical approaches.

Workshop Materials

Day 1:

  • Concept of scRNA-seq and main applications
  • Important issues in experimental design
  • Comparison between popular technical platforms
  • Raw data processing

Day 2: 

  • Overview of scRNA-Seq analysis and logistics of Scanpy;
  • Data preprocessing: loading, QC/filtering, normalization/scaling;
  • Dimensionality reduction and clustering;
  • Identification of marker genes;
  • Visualizations.

Pitfalls and considerations

Techinical Requirements

Students should have a working copy of Python3 with the Scanpy, Numpy, Pandas, and Matplotlib packages installed. An integrated development environment (IDE) for Python, such as PyCharm or Spyder is also recommended.


Dr. Breanne Sparta is a postdoctoral fellow at UCLA, in the lab of Professor Eric Deeds. Breanne’s research explores theories of biological organization and variation. Their current research centers questions of how cellular identities are realized. Breanne completed her B.S. in Biochemistry at Northeastern University and her Ph.D. at the University of California, Davis, where she studied the coordination of growth and metabolism in single, living cells. Email:



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Workshop Details

Prerequisites: Experience with Python is helpful, but not required.
Length:  3 days, 3 hrs per day
Level: Intermediate
Location: ZOOM
Seats Available: TBD

Fall 2020 Dates

November 9, 10, and 12
1:30 PM to 4:30 PM