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Slingshot Specifications

Process Details

  • Name: slingshot
  • Process UUID: 9a3946a7e5d1497fad34274187193127
  • Process Group: SingleCell

Overview

Slingshot is a trajectory inference method designed to identify and characterize developmental trajectories in single-cell RNA sequencing data. This process performs pseudotime analysis to infer cellular differentiation paths and developmental progressions by constructing smooth curves through clusters in reduced dimensional space.

This process is implemented in Bash, which invokes an R script for trajectory inference analysis using the Slingshot algorithm.

Key Functionality

  • Trajectory Inference: Constructs developmental trajectories through cell clusters using minimum spanning tree approaches
  • Pseudotime Calculation: Assigns pseudotime values to individual cells based on their position along inferred trajectories
  • Lineage Detection: Identifies multiple branching lineages and bifurcation points in developmental processes

Input/Output Specification

Inputs

Required Inputs

  • RDS File
    • Description: Seurat object containing single-cell RNA-seq data with dimensionality reduction and clustering results
    • Format: RDS

Outputs

  • RDS File
    • Description: Updated Seurat object containing trajectory inference results, pseudotime assignments, and lineage information
    • Format: RDS

Parameters & Settings

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

  • Reduction
    • Description: Reduction to use in slingshot analysis
    • Available options: umap (default), tsne

References & Resources

  • Tool Documentation: Contact the team for details on slingshot_analysis.R
  • Related Papers: Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018). https://doi.org/10.1186/s12864-018-4772-0