metabolicpathwayactivity
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.
npx skills add majiayu000/claude-skill-registry --skill metabolicpathwayactivity --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# MetabolicPathwayActivity Process Configuration ## Purpose 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. ## When to Use - **Third step in metabolic workflow**: After MetabolicInput and MetabolicExprImputation (optional) - **To quantify pathway-level metabolism**: When you need scores for each metabolic pathway per group - **Compare metabolic states**: To identify differences in pathway activity between clusters, treatments, or conditions - **Metabolic profiling visualization**: When you need heatmaps showing pathway activity across groups and violin plots showing distribution - **Comprehensive metabolic analysis**: As part of the ScrnaMetabolicLandscape group for complete metabolic landscape analysis ## Configuration Structure ### Process Enablement MetabolicPathwayActivity is part of the ScrnaMetabolicLandscape group. Enable it by enabling the group: ```toml [ScrnaMetabol
- Purpose
- When to Use
- Configuration Structure
- Process Enablement
- Input Specification
- Environment Variables
- Pathway Activity Scoring
- Scoring Method
- Scoring Process
- GMT File Sources
- Configuration Examples
- Minimal Configuration (Default Settings)
- Custom Plots with High Resolution
- Treatment Comparison Analysis
What does the metabolicpathwayactivity skill do?
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.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill metabolicpathwayactivity --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.