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bulk-rnaseq-activity-inference

Infer transcription factor and pathway activities from bulk RNA-seq results with DecoupleR.

1|Updated Nov 20, 2025
Search Tags:#bulk-rnaseq#tf-activity#decoupleR#progeny#ulm#mlm#omnipath
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill bulk-rnaseq-activity-inference
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bulk-rnaseq-activity-inference
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/bulk-rnaseq-activity-inference
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill bulk-rnaseq-activity-inference

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This skill automates the inference of regulatory activity from bulk RNA-seq differential expression results by computing transcription factor activities (ULM + CollecTRI) and signaling-pathway activities (PROGENy MLM) and preparing master tables for downstream analyses and publication-ready visuals.

Core Features & Use Cases

  • TF activity inference: DecoupleR ULM with CollecTRI regulons to generate per-TF activity scores and associated statistics.
  • PROGENy pathway inference: MLM-based activity scores for 14 canonical pathways using PROGENy footprints.
  • Master tables: Produces master_tf_activities.csv and master_progeny_activities.csv for integrated visualization and reporting.
  • Visualization readiness: Generates figures and supports interactive pathway exploration in downstream steps.
  • Integration ready: Builds data structures compatible with downstream explorers and GSEA complements.

Quick Start

Provide your differential expression results to run TF activity and PROGENy analyses and output master tables and figures.

Frequently Asked Questions about bulk-rnaseq-activity-inference

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

FAQPage Schema
How do I infer transcription factor activities from bulk RNA-seq differential expression results?▼

To infer transcription factor activities from bulk RNA-seq, provide your differential expression results to compute per-TF scores using the DecoupleR framework with ULM and CollecTRI regulons.

What is PROGENy pathway activity inference and how does it work with bulk RNA-seq?▼

PROGENy pathway activity inference computes signaling pathway scores from bulk RNA-seq data using MLM-based footprints for 14 canonical pathways, generating per-pathway activity scores and statistics.

Can I use DecoupleR with OmniPath networks for bulk RNA-seq regulatory analysis?▼

Yes, DecoupleR integrates with OmniPath networks to infer regulatory activities from bulk RNA-seq, combining CollecTRI regulons for TF activity and PROGENy footprints for pathway activity.

How do I generate publication-ready visuals and master tables from bulk RNA-seq data?▼

Generate publication-ready visuals and master tables by running TF activity and PROGENy analyses on your bulk RNA-seq differential expression results, outputting master_tf_activities.csv and master_progeny_activities.csv.

What's the best way to compute signaling pathway scores from bulk RNA-seq differential expression?▼

The best way to compute signaling pathway scores is applying PROGENy MLM-based inference to bulk RNA-seq differential expression results, producing activity scores for 14 canonical pathways with associated statistics.

Do I need differential expression results to run TF and pathway activity inference?▼

Yes, you need bulk RNA-seq differential expression results as input to compute TF activities via ULM with CollecTRI and pathway activities via PROGENy MLM, generating master tables and figures.

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