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This hands-on workshop will cover the basics of single-cell RNA-Seq analysis, using the Galaxy platform. Starting from a table of gene counts we will evaluate, filter, annotate and visualise the data. We will also cover clustering, cell type identification and differential expression.

Galaxy Australia is a platform that provides a simple and user-friendly interface to bioinformatics tools. The output we will generate is suitable for further analysis within Galaxy Australia, or locally.

Recommended Participants

Life scientists planning or running single cell RNAseq experiments (or mining public data), who want to perform their own analyses. All analysis is performed via the web browser. 

Participants should have a basic understanding of single cell RNAseq technology. No bioinformatics, programming, command line or single cell RNAseq analysis experience is expected. Previous experience using Galaxy is helpful but not required.

Learning Objectives

  • Understand the steps required in a typical single-cell RNA-Seq analysis
  • Determine and apply appropriate QC thresholds
  • Take a counts matrix, apply filtering, run UMAP and plot the results
  • Generate cell clusters and identify marker genes for cell type identification
  • Run a basic differential expression analysis
  • Understand the iterative nature of single-cell RNA-Seq analysis
  • Understand how single-cell RNA-Seq data and annotations can be saved in AnnData format and shared


  • Introduction to single-cell RNA-Seq analysis and Galaxy
  • QC and filter a counts matrix
  • Reduce dimensionality: PCA and UMAP 
  • Clustering
  • Basic differential expression
  • Plotting and visualisations
  • Options for further analysis

Upcoming workshops

Single-cell RNA-Seq Analysis using Galaxy

4 July, 9:00 am to 5:00 pm