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bulk-rnaseq-pathway-explorer

Convert unified RNaseq results into standalone interactive HTML pathway dashboards.

1|Updated Nov 20, 2025
Search Tags:#html#plotly#umap#interactive-dashboard#gsea#bulk-rnaseq#pathway-explorer
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill bulk-rnaseq-pathway-explorer
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bulk-rnaseq-pathway-explorer
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/bulk-rnaseq-pathway-explorer
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill bulk-rnaseq-pathway-explorer

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Turning unified RNaseq results into self-contained interactive HTML dashboards enables researchers to explore and share pathway insights without requiring specialized tooling or locally installed software.

Core Features & Use Cases

  • Converts master_unified.csv (or the legacy trio: master_gsea_table.csv, master_tf_activities.csv, and master_progeny_activities.csv) into standalone interactive HTML dashboards that can be opened in any browser.
  • Produces per-contrast HTML files (and an index) with embedded data, supports filtering by database and entity type, and renders interactive Plotly visualizations for pathway exploration.
  • Ideal for collaborating with non-R users, debugging pathway results, or publishing interactive analyses from RNaseq experiments.

Quick Start

Run the pathway-explorer CLI on your project using the master input to generate the interactive HTML dashboard.

Frequently Asked Questions about bulk-rnaseq-pathway-explorer

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

FAQPage Schema
How do I create an interactive HTML dashboard from bulk RNaseq pathway results?▼

You can create an interactive HTML dashboard from bulk RNaseq data by processing master_unified.csv into standalone HTML files with embedded Plotly visualizations for browser-based viewing.

Can I share RNaseq pathway analysis results with non-R users?▼

You can share RNaseq pathway results with non-R users by generating self-contained interactive HTML dashboards that embed all data and render Plotly visualizations directly in any standard web browser.

What input format is needed to generate a pathway explorer HTML file?▼

The input format needed to generate a pathway explorer HTML file is a master_unified.csv file, or the legacy trio of master_gsea_table.csv, master_tf_activities.csv, and master_progeny_activities.csv.

Does the interactive pathway dashboard require an internet connection to view?▼

Viewing the interactive pathway dashboard requires an internet connection to load Plotly from CDN, although all RNaseq data is embedded directly within the standalone HTML file.

Are the generated pathway explorer HTML files filtered by contrast and database?▼

The pathway explorer generates per-contrast HTML files and an index, supporting filtering by database and entity type to explore specific RNaseq pathway interactions.

What is the best way to debug GSEA pathway results from a bulk RNaseq experiment?▼

The best way to debug GSEA pathway results is to convert master_unified.csv into an interactive HTML dashboard, allowing you to visually explore per-contrast pathway activities and filter entities.

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