MouSSE R package

MouSSE estimates cell-level cytokine activity in murine single-cell RNA sequencing and spatial transcriptomics data using a gene set scoring approach with cytokine-specific gene sets constructed from experimental cytokine stimulation data.

Key Features:

• Cytokine Activity Estimation: MouSSE estimates the cell-level activity of 86 distinct cytokines.
• Gene Set Scoring: Cytokine-specific gene sets are constructed using experimental cytokine stimulation data from the Immune Dictionary.
• Modified VAM Technique: Cell-level scores are computed using a modification of the Variance-adjusted Mahalanobis (VAM) technique that supports both positive and negative gene weights.
• Cross-Species Extension: MouSSE extends the previously proposed SCAPE method from human to murine single-cell transcriptomics data.

Scientific Applications:

• Immune-Mediated Conditions: MouSSE enables understanding of signaling processes underpinning auto-immune disease, cancer, and response to infection.
• Murine scRNA-seq Analysis: MouSSE performs cytokine activity estimation in murine single-cell RNA-sequencing data.
• Murine Spatial Transcriptomics Analysis: MouSSE performs cytokine activity estimation in murine spatial transcriptomics data.

Methodology:

MouSSE constructs cytokine-specific gene sets using experimental cytokine stimulation data from the Immune Dictionary and computes cell-level scores using a modification of the Variance-adjusted Mahalanobis (VAM) technique that supports both positive and negative gene weights. Validation is performed via stratified cross-validation against the Immune Dictionary and against 10 cytokine activity estimation methods using external scRNA-seq and ST datasets.