Welcome to Cedar-Sinai Medical Center Data Science Navigation team’s Galaxy documentation!

In this tutorial, the user will be guided through using a workflow in the Cedars-Sinai Galaxy instance. This workflow is for Single-cell RNA-seq analysis, and covers Primary, Secondary and Tertiary analysis. In Galaxy, there are two workflows, “Single-cell RNA-seq Primary analysis” which covers Primary and secondary analysis and “Single-cell RNA-seq Tertiary analysis” which covers tertiary analysis. If you would like to access all tutorials developed for Galaxy workflows by the DSN team, it is accessible here.

Note

This project is under active development.

Contents

• Single-cell RNA-seq introduction
• Quick-start
• Primary analysis
  • Using example data
  • Importing data
  • Quality check
• Secondary Analysis
  • Alignment and Quantification of reads
  • Quality control of single-cell results
• Tertiary analysis
  • Importing data
    • Importing data from Primary Analysis
    • Importing example data for running Tertiary Analysis
  • Brief tutorial on filtering data
  • Filter data
  • Normalize data
  • Find variable genes
  • Scale data
  • Run PCA and Build a neighborhood graph
  • Run UMAP and tSNE
  • Find clusters
  • Find markers
  • Plot PCA, UMAP and tSNE
  • Annotate gene names in cluster file
• Conclusion