GEO Plugin

A Chrome browser extension that detects GEO accession numbers on research journal pages and surfaces them in an interactive panel — complete with a hierarchical series/sample tree, BigWig file selection, and one-click IGV genome browser launch.

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Purpose

Genomics researchers frequently encounter GEO accession numbers (GSE, GSM, GPL, GDS, GSL) embedded in journal articles, preprints, and supplementary materials. Navigating from a citation to the actual data on NCBI requires multiple clicks and context switches. GEO Plugin eliminates that friction by:

• Automatically scanning any page for GEO accession numbers
• Displaying a count badge and a slide-in panel listing every accession found
• Expanding GSE series into their super-series / sub-series / sample hierarchy (fetched live from NCBI)
• Identifying BigWig (.bw / .bigwig) supplementary files within individual samples
• Letting researchers select files into a cart and open them directly in an embedded IGV genome browser

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Tech Stack

Layer	Technology
Extension platform	Chrome Extension — Manifest V3
Runtime language	Vanilla JavaScript (ES2020, no build step)
Styling	Plain CSS (all selectors namespaced geo-plugin-)
Genome data API	NCBI GEO SOFT text format (acc.cgi?form=text)
Genome browser	IGV.js v3 (loaded via jsDelivr CDN at checkout time)
Icons	PNG (generated via PowerShell System.Drawing)

No npm, no bundler, no framework. The extension installs as a directory of static files.

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Installation (Development)

1. Clone the repository

   git clone https://github.com/treznicek/GEO_Plugin.git
   cd GEO_Plugin
   

2. Load into Chrome

   • Open chrome://extensions
   • Enable Developer mode (toggle, top-right)
   • Click Load unpacked and select the GEO_Plugin directory

3. Test it

   • Navigate to any genomics article — e.g. https://pmc.ncbi.nlm.nih.gov/articles/PMC12136341/
   • A red badge appears in the bottom-right corner showing the count of GEO accessions found
   • Click the badge to open the panel

4. After editing source files

   • Return to chrome://extensions and click the refresh icon on the GEO Plugin card
   • Reload the target browser tab

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Core Architecture

GEO_Plugin/
├── manifest.json       Extension entry point (Manifest V3)
├── content.js          Single content script — all runtime logic
├── content.css         All styles, injected alongside content.js
├── icons/
│   ├── icon16.png
│   ├── icon48.png
│   └── icon128.png
├── NOTICE              Third-party attribution (IGV.js)
├── CONTRIBUTING.md     Contributor guide
├── .github/
│   └── CODEOWNERS      Code review assignments
└── .gitignore

content.js — functional sections

Section	Responsibility
Accession scan	Regex /\b(GSE|GSM|GPL|GDS|GSL)\d+\b/g run against document.body.innerText; deduplication via Set
Badge	Fixed red circle (#geo-plugin-badge) — hides on panel open, reappears on close
Panel	Slide-in drawer (#geo-plugin-panel) with dark overlay; lazy-created on first badge click
GSE tree	Expand button fetches NCBI SOFT text, parses title / super-series / sub-series / sample IDs
GSM nodes	Each sample is expandable; fetches GSM SOFT text to find BigWig supplementary files
Cart	In-memory Map (url → metadata); sticky footer shows count + "Open in IGV" button
IGV checkout	Generates a self-contained HTML blob with IGV.js pre-configured with selected tracks; opens in a new tab

Data flow

Page load
  └─ Scan innerText for GEO accessions
       └─ Badge rendered (count)
            └─ User clicks badge → Panel opens
                 └─ GSE accession clicked (▶)
                      └─ fetch NCBI SOFT text (GSE)
                           ├─ Render: title, super/sub-series, sample list
                           └─ GSM accession clicked (▶)
                                └─ fetch NCBI SOFT text (GSM)
                                     └─ Render: BigWig file checkboxes
                                          └─ User checks files → Cart updated
                                               └─ "Open in IGV" → Blob URL → New tab

Key constants and utilities (content.js)

Symbol	Purpose
ACCESSION_RE	Master regex for all GEO accession types
GEO_URL	Base link to NCBI GEO accession viewer
GEO_TEXT_BASE	Base URL for NCBI SOFT text API
MAX_SAMPLES_SHOWN	Max GSM rows rendered inline (default 10)
cart	Map<url, {name, gsm, gse, organism}> — selected BigWig files
gseFiles	Map<gse, Set<url>> — all fetched BigWig URLs per series
fileIndex	Map<url, metadata> — flat lookup used by "Add all loaded"
ORGANISM_GENOME	Maps organism strings to IGV genome IDs
fetchGEOSeries(acc)	Fetches and parses a GSE SOFT record
parseGsmSoft(text)	Parses a GSM SOFT record for BigWig URLs and organism
buildIgvHtml(entries)	Generates the IGV viewer HTML blob

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Third-Party Notices

See NOTICE for third-party attribution.

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License

MIT — see LICENSE.