STARS v2.0 Enhanced

Standards for Transcriptomic Analysis Reporting: Ensuring reproducibility in single-cell and spatial genomics

Shoumit Dey^1†*, Nidhi S. Dey^1†, Daniel Holbrook^1†, Paul M. Kaye^1*
1 York Biomedical Research Institute, Hull York Medical School, University of York, United Kingdom

^† These authors contributed equally

^* Correspondence: Shoumit Dey and Paul Kaye

Abstract

Single-cell and spatial transcriptomic data analysis workflows are often complex, involving multiple steps such as data preprocessing, normalization, dimensionality reduction, clustering, and visualization. The diversity of tools and methods used across studies makes it challenging for researchers to replicate workflows, compare analyses, or adopt best practices. Here, we present STARS (Scientific Standards for Transcriptomic Analysis Reporting), a comprehensive metadata collection tool designed to ensure reproducibility and standardization in single-cell and spatial transcriptomic studies. STARS provides an interactive HTML-based interface that guides researchers through documenting their analysis workflows according to standardized reporting criteria. The tool captures essential metadata including study design, sample information, quality control parameters, analysis pipeline details, software versions, and data availability. Users can visualize their analysis pipelines through automatically generated flowcharts and export their documentation in structured JSON format. The exported JSON metadata or the interactive HTML interface can be directly uploaded to repositories such as Figshare when submitting manuscripts for peer review or publication, facilitating transparency, enhancing reproducibility, and enabling the comparison of workflows across studies. By standardizing the way transcriptomic analysis pipelines are documented and shared, STARS promotes best practices in computational biology and supports the growing need for reproducible research in single-cell and spatial genomics.

Overview

STARS (Scientific Standards for Transcriptomic Analysis Reporting) is a comprehensive metadata collection tool designed to ensure reproducibility and standardization in single-cell and spatial transcriptomic studies. This HTML-based interface provides an interactive form for researchers to document their analysis workflows according to STARS v2.0 standards.

Features

📋 Form-Based Metadata Collection

• Essential Fields: 15 required fields for STARS compliance
• Recommended Fields: 12 additional fields for enhanced documentation
• Real-time Progress Tracking: Visual progress bars showing completion status
• Field Validation: Automatic validation with visual indicators

🧬 Pre-loaded Example Dataset

• Complete example study demonstrating STARS-compliant documentation
• Single-click loading of example data
• Demonstrates best practices for metadata reporting

🔍 Quality Control Documentation

• Cell filtering parameters (min genes, max mitochondrial %, min UMI)
• Doublet detection methods
• Batch correction strategies

⚙️ Analysis Pipeline Documentation

• Normalization methods
• Clustering algorithms and resolution parameters
• Dimensionality reduction techniques (PCA, UMAP, t-SNE, etc.)
• Gene selection criteria

📊 Interactive Pipeline Visualization

• Flowchart Generation: Automatically generates Mermaid flowcharts based on your metadata
• Visual representation of your analysis workflow
• Color-coded steps (QC, Analysis, Results)

💾 Export Functionality

• JSON Export: Generate structured STARS-compliant JSON reports
• Timestamped exports
• Includes validation scores and completeness metrics

🎨 Modern User Interface

• Scientific-themed design with molecular-inspired aesthetics
• Responsive layout for desktop and mobile devices
• Smooth animations and transitions
• Autocomplete suggestions for common values

Usage

Online Access

🌐 Access STARS v2.0 Enhanced online: https://jipsi.github.io/STARS/

The tool is freely hosted on GitHub Pages and can be accessed directly from your web browser without any installation.

Getting Started

1. Access the tool either:
   • Online: Visit https://jipsi.github.io/STARS/ (recommended)
   • Locally: Download and open STARS_v2_enhanced.html in any modern web browser (Chrome, Firefox, Safari, Edge)
2. Load Example Data (optional): Click the "📋 Load Example" button to see a complete example
3. Fill in the Form: Complete the essential fields (marked with *) for STARS compliance
4. Track Progress: Monitor your completion status using the progress bars
5. Validate: Click "✅ Validate Form" to check for missing required fields
6. Visualize: Click "📊 Generate & Visualize Pipeline" to see your workflow as a flowchart
7. Export: Click "💾 Export STARS Report" to download your metadata as JSON

Form Sections

1. 🔬 Study Information (Essential)

   • Study title, type, objectives, keywords
   • DOI and funding information (recommended)

2. 🧪 Sample Information (Essential)

   • Sample size, tissue type, species, sequencing technology
   • Experimental conditions and ethics approval (recommended)

3. 🔍 Quality Control (Essential)

   • Cell filtering parameters
   • Doublet detection methods
   • Batch correction (recommended)

4. ⚙️ Analysis Pipeline (Essential)

   • Normalization and clustering methods
   • Dimensionality reduction techniques
   • Random seed and gene selection (recommended)

5. 💻 Software & Environment (Essential)

   • Primary software and versions
   • Runtime environment
   • Additional packages and compute environment (recommended)

6. 📂 Data & Code Availability (Essential)

   • Data and code repository information
   • Access restrictions and licensing (recommended)

Keyboard Shortcuts

• Ctrl/Cmd + S: Validate form
• Ctrl/Cmd + Shift + Enter: Generate and visualize pipeline
• Ctrl/Cmd + Shift + E: Export STARS report
• Escape: Close modal windows

Autocomplete

The form includes autocomplete suggestions for:

• Study types (Single-cell RNA-seq, Spatial transcriptomics, etc.)
• Tissue types (Brain cortex, PBMC, Kidney, etc.)
• Species (Homo sapiens, Mus musculus, etc.)
• Sequencing technologies (10X Genomics, Smart-seq2, etc.)
• Analysis methods (Seurat, Scanpy, DoubletFinder, etc.)

Technical Details

Requirements

• Modern web browser with JavaScript enabled
• Internet connection (for loading Google Fonts and Mermaid.js library)

Hosting

STARS v2.0 Enhanced is hosted on GitHub Pages at https://jipsi.github.io/STARS/. The page is automatically updated whenever changes are pushed to the main branch. You can also download the HTML file and host it on any web server or use it locally.

Dependencies

• Mermaid.js (v10.6.1): For flowchart generation
• Google Fonts: JetBrains Mono and Crimson Pro

Browser Compatibility

• Chrome/Edge (recommended)
• Firefox
• Safari
• Opera

Data Storage

• Form data is automatically saved to browser localStorage every 30 seconds
• Data persists between browser sessions
• Use "🗑️ Clear Form" to remove saved data

Output Format

The exported JSON follows a structured schema including:

{
  "@context": {...},
  "@type": "stars:ResearchProject",
  "metadata": {
    "standard": "STARS",
    "version": "2.0",
    "generated": "ISO timestamp",
    "generator": "STARS v2.0 Enhanced Interface"
  },
  "study": {...},
  "sample": {...},
  "qualityControl": {...},
  "analysis": {...},
  "software": {...},
  "availability": {...},
  "validation": {
    "essentialComplete": 15,
    "recommendedComplete": 12,
    "completenessScore": 1.0
  }
}

Example Study

The included example demonstrates a complete single-cell RNA-seq study:

• Sample Type: Human brain organoids
• Technology: 10X Genomics 3' v3
• Cells: ~15,000 cells
• Analysis: Seurat + Cell Ranger
• Pipeline: SCTransform normalization, Leiden clustering, Harmony batch correction

STARS Compliance

To achieve STARS compliance:

• ✅ Complete all 15 essential fields
• 📋 Complete recommended fields for enhanced documentation
• ✅ Validate your form before export
• 📊 Review the generated pipeline flowchart

Notes

• The form includes expandable sections for recommended fields
• Progress is tracked in real-time as you fill in fields
• Validation indicators (✓ and !) show field status
• The flowchart visualization updates based on your input

Version

STARS v2.0 Enhanced - Current version with improved UI, flowchart visualization, and enhanced validation.

License

This tool is provided for research use. Please refer to your institution's policies regarding data sharing and metadata standards.

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For questions or issues, please refer to the STARS documentation or contact your research team.