bulk-rnaseq-activity-inference
CommunityInfer TF and pathway activities from bulk RNA-seq.
Authortony-zhelonkin
Version1.0.0
Installs0
System Documentation
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.
Dependency Matrix
Required Modules
None requiredComponents
references
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: bulk-rnaseq-activity-inference Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#bulk-rnaseq-activity-inference Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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