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Getting Started with Cell Ranger

Getting Started with Cell Ranger

Fixed RNA Profiling has been renamed Flex. All future updates, documentation, and support will reference Flex.
Barcode Enabled Antigen Mapping (BEAM) is unsupported with GEM-X chemistry; therefore, Cell Ranger does not support BEAM/Antigen Capture libraries produced with this chemistry.
  1. 1

    Introduction

    What is Cell Ranger?Supported librariesWhat is Feature Barcode?What is Flex?What is Sample Multiplexing?What is Cell Type Annotation?What is Antigen Capture (BEAM)?What is HT (High Throughput)?Experimental design for Immune Profiling
  2. 2

    Set up

    System requirementsDownloadInstallCloud Analysis
  3. 3

    Pipelines and inputs

    Choose a pipelineIdentify input filesCommand line arguments
  4. 4

    Review outputs

    Output file overview
  5. 5

    Other resources

    TutorialsGlossaryAdvancedPublic datasets