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decoupler-activity-visualization

Visualize DecoupleR TF and PROGENy pathway activity results as plots and README summaries.

1|Updated Nov 20, 2025
Search Tags:#visualization#ggplot2#barplot#volcano-plot#tf-activity#progeny#decoupler
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill decoupler-activity-visualization
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: decoupler-activity-visualization
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/.deprecated/decoupler-activity-visualization
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill decoupler-activity-visualization

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Visualize DecoupleR TF activity and PROGENy pathway activity results to produce publication-quality plots and interpretation summaries.

Core Features & Use Cases

  • Generate publication-quality barplots, volcano plots, and distributions for TF activity (DecoupleR ULM) and PROGENy pathway activity (MLM).
  • Create interpretation README files and summary tables to accompany figures.
  • Facilitate quick exploratory analysis by producing consistent visualizations and ready-to-share outputs.

Quick Start

Provide your upstream results (master_tf_activities.csv and master_progeny_activities.csv) and run the visualization scripts to generate plots and README.

Frequently Asked Questions about decoupler-activity-visualization

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I visualize DecoupleR TF activity results for publication?▼

To visualize DecoupleR TF activity results, you need upstream analysis outputs like master_tf_activities.csv to generate publication-quality barplots, volcano plots, and target-gene scatter plots.

What plots are needed to show PROGENy pathway activity effectively?▼

PROGENy pathway activity is effectively shown using publication-quality barplots, volcano plots, and distribution histograms generated from upstream master_progeny_activities.csv analysis results.

Can I generate interpretation summaries alongside TF activity volcano plots?▼

Yes, generating interpretation summaries alongside TF activity volcano plots is supported. The process automatically creates README files and summary tables to accompany your visual outputs.

Do I need pre-computed CSV files to create PROGENy activity barplots?▼

Yes, you need pre-computed CSV files. Generating PROGENy activity barplots requires upstream master_progeny_activities.csv files produced by dedicated pathway analysis steps.

What is the best way to share DecoupleR ULM analysis outputs with collaborators?▼

The best way to share DecoupleR ULM analysis outputs is by generating ready-to-share visualizations and interpretation README files that provide consistent, publish-ready figures and summary tables.

Why does my TF activity visualization fail without upstream analysis results?▼

TF activity visualization fails without upstream results because the plotting scripts strictly require master_tf_activities.csv and master_progeny_activities.csv files produced by prior dedicated analysis steps.

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