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SCEtoLOOM Specifications

Process Details

  • Name: SCEtoLOOM
  • Process UUID: RhLXg239zuwwAJebwzqAEfBtxHzDww
  • Process Group: SingleCell

Overview

This process converts single-cell RNA-seq analysis results into a loom file format. It takes SingleCellExperiment objects or Seurat objects stored as RDS files and generates loom files that are compatible with downstream analysis tools and visualization platforms.

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

Key Functionality

  • Data Format Conversion: Transforms Seurat or SingleCellExperiment objects into loom file format
  • Gene Annotation Integration: Incorporates gene annotation data including Ensembl IDs from external reference sources
  • Data Quality Control: Filters out genes with zero expression across all cells to reduce file size
  • Metadata Preservation: Maintains cell-level metadata from the original analysis object

Input/Output Specification

Inputs

Required Inputs

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

Outputs

  • Output File
    • Description: Converted single-cell data in loom file format suitable for visualization and further analysis
    • 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. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 36, 411-420 (2018). DOI: 10.1038/nbt.4096