Analysis Guides
Jun 3, 2022

Hands-on Tour of the Single Cell Analysis Journey, From Cloud to Loupe to Community-Developed Tools

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Note: 10x Genomics does not provide support for community-developed tools and makes no guarantees regarding their function or performance. Please contact tool developers with any questions. If you have feedback about Analysis Guides, please email [email protected].


In this workshop, you will be introduced to the single cell gene expression analysis journey. Analysis begins at experimental design. Together we will explore a set of neutrophil data starting with the 10x Cloud Analysis platform for raw data processing. From there, we will assess the data quality using the Cell Ranger web summary and then move into the Loupe Browser for our initial analysis. We will take what we have learned from the Loupe analysis into the community-developed tools space where we will further explore neutrophil cell development with an RNA velocity analysis. To wrap things up, each participant will have the opportunity to map out their own analysis journey moving forward by sitting down with members of the Applied Bioinformatics team from 10x Genomics and local onsite bioinformaticians.



  • Introduction to the workshop and housekeeping
  • 10x Genomics Cloud Analysis: from FASTQs to Quantitative Biological Information with Cell Ranger
  • Break
  • Introduction to Single Cell RNA-seq Data Analysis
  • Quality assessment: interpreting the Cell Ranger web summary
  • Lunch
    • Have some food and get to know the folks in the room better