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MubasherMohammed
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diff-visualizer

Generate visualizations and reports for bulk and single-cell RNA-seq differential expression.

Updated May 10, 2026
Search Tags:#volcano plot#differential-expression#heatmap#visualisation#scrna#rnaseq
One-click install
npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill diff-visualizer
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: diff-visualizer
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/diff-visualizer
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill diff-visualizer

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, numpy, matplotlib, anndata, scanpy, pypdf, pdfplumber, pdf2image, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies the process of visualizing RNA-seq and single-cell RNA-seq differential expression results, enabling users to quickly generate publication-quality figures and reports.

Core Features & Use Cases

  • Bulk RNA Visualization: Generate volcano plots, MA plots, top-gene bars, and heatmaps for bulk RNA-seq differential expression.
  • scRNA Visualization: Create dataset-level contrast volcanoes, within-cluster comparison panels, marker ranking bars, and AnnData-based enhancement plots for single-cell RNA-seq.
  • Reporting: Automatically generate HTML/Markdown reports, including report.md, report.html, result.json, and reproducibility files.
  • Use Case: Suppose you have completed a bulk RNA-seq analysis and want to visualize the results. You can use this Skill to automatically generate a comprehensive report with all relevant figures and tables.

Quick Start

Run the diff-visualizer skill with the input file 'de_results.csv' and output the report to 'output_report'.

Frequently Asked Questions about diff-visualizer

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

FAQPage Schema
How do I generate volcano plots and heatmaps from bulk RNA-seq differential expression results?▼

Generate volcano plots and heatmaps from bulk RNA-seq differential expression results by providing a CSV file of DE outputs to the skill, which automates figure creation using pandas and matplotlib.

Can I visualize single-cell RNA-seq differential expression within specific clusters?▼

You can visualize single-cell RNA-seq differential expression within specific clusters by processing AnnData objects with scanpy to produce within-cluster comparison panels and marker ranking bars.

How do I automatically create a publication-quality report for RNA-seq analysis?▼

Automatically create a publication-quality report for RNA-seq analysis by running the skill on your differential expression inputs, which outputs formatted HTML, Markdown, and JSON result files.

Does this visualization tool work with AnnData objects for scRNA-seq?▼

This visualization tool works directly with AnnData objects for scRNA-seq by leveraging scanpy to generate dataset-level contrast volcanoes and AnnData-based enhancement plots.

What is the best way to visualize large-scale RNA-seq differential expression data?▼

The best way to visualize large-scale RNA-seq differential expression data is to use an automated Python-based pipeline that processes sequencing files with numpy and generates comprehensive visual reports.

Do I need a specific CSV format to visualize RNA-seq differential expression results?▼

You need a differential expression results CSV file, such as 'de_results.csv', containing the necessary statistical columns for the tool to generate volcano plots and heatmaps.

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