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Fitgam Specifications

Process Details

  • Name: fitgam
  • Process UUID: af6d8d2f755b4b70a71f23adfba945f5
  • Process Group: SingleCell

Overview

The fitgam process performs trajectory analysis on single-cell RNA sequencing data using the Slingshot algorithm. This process fits generalized additive models (GAMs) to genes along pseudotime trajectories to identify genes with dynamic expression patterns during cellular differentiation or developmental processes. It is particularly useful for understanding gene expression changes along continuous biological processes in single-cell datasets.

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

Key Functionality

  • Trajectory Fitting: Fits smooth curves (GAMs) to gene expression data along pseudotime trajectories
  • Dynamic Gene Identification: Identifies genes with significant expression changes along developmental trajectories
  • Variable Gene Selection: Allows filtering to top variable genes for computational efficiency on large datasets
  • Statistical Modeling: Provides statistical assessment of gene expression dynamics using generalized additive models

Input/Output Specification

Inputs

Required Inputs

  • RDS File (Object)

    • Description: Single-cell RNA sequencing data object containing expression data and metadata
    • Format: RDS

  • RDS File (SCE)

    • Description: SingleCellExperiment object with trajectory information from Slingshot analysis
    • Format: RDS

Outputs

  • RDS File Set
    • Description: Collection of RDS files containing fitted GAM models and trajectory analysis results
    • Format: rds

Parameters & Settings

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

  • Number of Genes
    • Description: Number of top variable genes to use in fitgam analysis. If empty, all of top variable genes will be used. Set this value for big datasets to make the analysis faster.
    • Default value: (empty - uses all top variable genes)

References & Resources

  • Tool Documentation: Contact the team for details on fitgam.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