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SCEto LOOM Specifications

Process Details

  • Name: SCEto LOOM
  • Process UUID: RhLXg239zuwwAJebwzqAEfBtxHzDww
  • Process Group: SingleCell

Overview

This process converts single cell RNA-Seq analysis results (SingleCellExperiment object or Seurat object) into a Loom file format. The process filters genes, creates annotation tables using Ensembl biomaRt, and generates a Loom file that can be used for downstream analysis tools and visualization platforms.

This process is implemented in Bash, which invokes an R script for data conversion using Seurat and biomaRt packages.

Key Functionality

  • Data Format Conversion: Transforms Seurat or SingleCellExperiment objects into Loom format
  • Gene Annotation: Creates comprehensive gene annotation tables using Ensembl biomaRt with gene IDs, names, and biotypes
  • Data Filtering: Removes genes with zero expression across all cells and handles duplicate gene names
  • Metadata Preservation: Maintains cell metadata from the original object in the output Loom file

Input/Output Specification

Inputs

Required Inputs

  • RDS File
    • Description: Single cell RNA-Seq analysis results stored as either a SingleCellExperiment object or Seurat object
    • Format: RDS

Outputs

  • Output File
    • Description: Loom file containing the converted single cell data with gene annotations and cell metadata
    • Format: out

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Generate Loom File
    • Description: Whether to generate a loom file from the final analysis results, the default is False
    • Available options: TRUE, FALSE (default)

References & Resources

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