metabolicpathwayactivity

What problem does it solve?

Calculates pathway activity scores for metabolic pathways across different cell groups and subsets. This process quantifies the metabolic activity of each pathway per group, generating visualizations (heatmaps and violin plots) to compare metabolic states between clusters or conditions. Based on the methodology from Xiao et al. (2019) Nature Communications.

Core Features & Use Cases

• AUCell-like scoring: ranks gene expression per cell and computes pathway activity scores using gene sets.
• Permutation-based significance: uses ntimes permutations to estimate p-values and normalize scores.
• Group and subset analysis: supports grouping by metadata (e.g., seurat_clusters) and optional subsetting (subset_by) for focused comparisons.
• Visualization: outputs heatmaps and violin plots to illustrate pathway activity across groups or conditions; can produce merged heatmaps for multiple subsets.
• Upstream and downstream integration: designed to work within the ScrnaMetabolicLandscape group alongside MetabolicInput and related processes.

Quick Start

Run MetabolicPathwayActivity after MetabolicInput to compute pathway scores and generate heatmaps and violin plots for your Seurat object.