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Supported Pipelines and Products

Supported Pipelines and Products

To help you decide how best to access the 10x Cloud for your use case, review the pipeline analyses that are currently supported for each method. The specific supported pipeline versions and library types are provided in the tables below this section.

Pipeline / Analysis10x Cloud Analysis web app10x Cloud Analysis Command Line (CLI) tool10x Cloud prompt-based interface
Cell Ranger count
Cell Ranger multi
Cell Ranger aggr
Cell Ranger vdj
Cell Ranger reanalyze
Cell Ranger ARC count
Cell Ranger ARC aggr
Cell Ranger ARC reanalyze
Space Ranger count
Automated cell type annotation (Specify whether to run along with Cell Ranger count or multi analyses) (Specify whether to run along with Cell Ranger count or multi analyses)
Data normalization (SCTransform)
Batch correction (Harmony)
Analysis PipelinesPipeline VersionLibrary Types
Space Ranger count

Visit the Space Ranger count documentation to learn more.
  • 4.0.1
  • 3.1
  • 3.0
  • Visium HD Spatial Gene Expression
  • Visium HD 3' Gene Expression
Cell Ranger count

Visit the Cell Ranger count documentation to learn more.
  • 9.0
  • 8.0
  • 7.2
  • 7.1
  • 7.0
  • 6.1
  • 6.0
  • 5.0
  • 4.0
  • 3.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • Custom Library
Cell Ranger multi

Visit the following pages to learn more about Cell Ranger multi with sample multiplexing data, Flex data, and V(D)J data.
  • 9.0
  • 8.0
  • 7.2
  • 7.1
  • 7.0
  • 6.1
  • 6.0
  • 5.0
  • 4.0
  • 3.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture
Cell Ranger aggr

Visit the Cell Ranger aggr documentation to learn more.
  • 9.0
  • 8.0
  • 7.2
  • 7.1
  • 7.0
  • 6.1
  • 6.0
  • 5.0
  • 4.0
  • 3.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture
Cell Ranger vdj

Currently, the 10x Cloud Platform does not support Cell Ranger vdj in de novo mode.

Visit the Cell Ranger vdj documentation to learn more.
  • 9.0
  • 8.0
  • 7.2
  • 7.1
  • 7.0
  • 6.1
  • 6.0
  • 5.0
  • 4.0
  • 3.1
  • Universal 5' V(D)J
Cell Ranger reanalyze1

Visit the Cell Ranger reanalyze documentation to learn more.
  • 9.0
  • 8.0
  • 7.2
  • 7.1
  • 7.0
  • 6.1
  • 6.0
  • 5.0
  • 4.0
  • 3.1
  • Universal 3' Gene Expression
  • Universal 5' Gene Expression
SCTransform/Harmony workflow for data integration
  • 1.0
  • Universal 3' Gene Expression
  • Universal 5' Gene Expression
  • Flex Gene Expression
Cell Ranger annotate (Beta)

Visit the Cell Ranger annotate documentation to learn more.
  • 0.2
  • Universal 3' Gene Expression
  • Universal 5' Gene Expression
  • Flex Gene Expression
Cell Ranger ARC count

Visit the Cell Ranger ARC count documentation to learn more.
  • 2.0
  • Epi Multiome ATAC + Gene Expression
Cell Ranger ARC aggr

Visit the Cell Ranger ARC aggr documentation to learn more.
  • 2.0
  • Epi Multiome ATAC + Gene Expression
Cell Ranger ARC reanalyze1

Visit the Cell Ranger ARC reanalyze documentation to learn
  • 2.0
  • Epi Multiome ATAC + Gene Expression

1At this time, reanalysis of aggregated analyses (Cell Ranger) is not available in Cloud Analysis for the web browser.

Analysis PipelinesPipeline VersionLibrary Types
Space Ranger count

Visit the Space Ranger count documentation to learn more.
  • 4.0.1
  • Visium HD Spatial Gene Expression
  • Visium HD 3' Gene Expression
Cell Ranger count

Visit the Cell Ranger count documentation to learn more.
  • 9.0.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • Custom Library
Cell Ranger multi

Visit the following pages to learn more about Cell Ranger multi with sample multiplexing data, Flex data, and V(D)J data.
  • 9.0.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture
Cell Ranger aggr

Visit the Cell Ranger aggr documentation to learn more.
  • 9.0.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture
Cell Ranger vdj

Currently, the 10x Cloud Platform does not support Cell Ranger vdj in de novo mode.

Visit the Cell Ranger vdj documentation to learn more.
  • 9.0.1
  • Universal 5' V(D)J
Cell Ranger ARC count

Visit the Cell Ranger ARC count documentation to learn more.
  • 2.1
  • Epi Multiome ATAC + Gene Expression
Cell Ranger ARC aggr

Visit the Cell Ranger ARC aggr documentation to learn more.
  • 2.1
  • Epi Multiome ATAC + Gene Expression
Analysis PipelinesPipeline VersionLibrary Types
Cell Ranger count9.0.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
Cell Ranger multi9.0.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture
Cell Ranger aggr9.0.1
  • Universal 3’ Gene Expression
  • Universal 5’ Gene Expression
  • Flex Gene Expression
  • Feature Barcode Libraries
    • Antibody Capture
    • CRISPR Guide Capture
    • Custom Library
    • Flex Antibody Capture
    • Flex CRISPR Guide Capture
  • Universal 5' V(D)J
  • Sample multiplexing
    • 3' CellPlex
    • On-chip multiplexing (OCM)
    • Hashing with Antibody Capture