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Seurat to SCE Copy Specifications

Process Details

  • Name: seurat_to_sce_copy
  • Process UUID: DJro1qNcmIXDmcHyDJBZtm3qB419qs
  • Process Group: SingleCell

Overview

This process converts a Seurat object to a SingleCellExperiment (SCE) object, enabling interoperability between different single-cell RNA sequencing analysis frameworks. This conversion is essential for workflows that need to transition from Seurat-based analyses to Bioconductor-based downstream processing using SingleCellExperiment infrastructure.

This process is implemented in R, utilizing the Seurat and SingleCellExperiment packages for object conversion.

Key Functionality

  • Object Format Conversion: Transforms Seurat objects into SingleCellExperiment objects while preserving data structure
  • Data Preservation: Maintains expression data, metadata, and dimensional reductions during conversion
  • Framework Interoperability: Enables seamless transition between Seurat and Bioconductor ecosystems

Input/Output Specification

Inputs

Required Inputs

  • Seurat Object
    • Description: A Seurat object containing single-cell RNA sequencing data with expression matrices, cell metadata, and analysis results
    • Format: RDS

Outputs

  • SingleCellExperiment Object
    • Description: A SingleCellExperiment object containing the converted single-cell data compatible with Bioconductor workflows
    • Format: RDS

Parameters & Settings

This process does not have user-configurable parameters.

References & Resources

  • Tool Documentation: Contact the team for details on the conversion script
  • Related Papers: Butler, A., Hoffman, P., Smibert, P., Papalexi, E., & Satija, R. (2018). Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nature Biotechnology, 36(5), 411-420.