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 Seurat;
  • 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 version of R installed (version 4.0.0 or higher) with the Seurat library installed and an Integrated Development Environment (IDE) for R, preferentially, RStudio.


Dr. Giovanni Quinones Valdez is part of the Xiao’s lab where his research focuses the study the function and regulation of nucleotide variants in RNA, specifically the analysis of NGS data to unveil biological mechanisms regulating post-transcriptional RNA modifications, and developing computational tools to study their function in the context of RNA processing. His expertise includes developing bioinformatic pipelines for the study of RNA biology in health and disease. Dr. Quinones Valdez earned his Bachelor of Science at the University of Florida in Biological Engineering, and his Ph.D. in Bioengineering at UCLA.Email:



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Workshop Details

Prerequisites: Intro to R (W3) is highly recommended.
Length:  3 days, 3 hrs per day
Level: Intermediate
Location: Boyer 529
Seats Available: 28

Spring 2022 Dates

May 3, 4, and 5
1:30 PM – 4:30 PM