zhongguojie1998

Weekly Genomics Literature Review — Claude Code Plugin

Automated pipeline that searches bioRxiv and top genomics journals, downloads full PDFs, and has Claude Code read them and produce critical reviewer-quality assessments with fine-grained scoring.

No API key needed — works entirely within Claude Code. The Python script only handles search and PDF download; Claude Code itself reads the PDFs and writes reviews.

Installation

First, install Claude Code in terminal using the following command (for details, refer to https://code.claude.com/docs/en/setup#installation)

curl -fsSL https://claude.ai/install.sh | bash

Next, start an interactive session of Claude Code

claude

For the step Select login method, Select Claude account with subscription, then it will automatically ask for account credentials and jump to the browser.

Finally, install directly from Claude Code's interactive session:

/plugin marketplace add zhongguojie1998/weekly-lit-review
/plugin install weekly-lit-review

Usage

Once installed, trigger the pipeline in any Claude Code session:

Note: It will consume tokens at the speed depending on the model you select. I recommend using /model haiku command first to set it to the lightest model before running the command.

/weekly-lit-review:weekly-lit-review --days 7
/weekly-lit-review:weekly-lit-review --max-papers 10
/weekly-lit-review:weekly-lit-review --days 3 --no-pdf

Results are saved to ~/Desktop/Claude/week-lit-review-results/.

Non-interactive (from terminal, experimental)

Run directly from the command line without entering an interactive session:

# Defaults: 7 days, 80 papers, sonnet model
bash scripts/run_review.sh

# Customize
bash scripts/run_review.sh --days 3 --max-papers 10
bash scripts/run_review.sh --days 7 --model opus
bash scripts/run_review.sh --days 7 --no-pdf

Pipeline Overview

┌──────────────┐     ┌──────────────┐     ┌──────────────┐     ┌──────────────┐     ┌──────────────┐
│  Read Config │────▶│ Search Papers│────▶│Download PDFs │────▶│Claude Reads  │────▶│ Write Report │
│  (YAML)      │     │ bioRxiv+RSS  │     │ (full text)  │     │ PDFs & Review│     │  (.md files) │
└──────────────┘     └──────────────┘     └──────────────┘     └──────────────┘     └──────────────┘

Step 1: Read Configuration

• Loads assets/config.yaml
• Configures search parameters: lookback days, max papers, categories, keywords
• Sets up journal RSS feed list and bioRxiv categories

Step 2: Search for Papers

• bioRxiv: Queries the bioRxiv content API for recent preprints in configured categories (genomics, genetics, bioinformatics)
• Journal RSS Feeds: Parses RSS feeds from 15 journals across Nature, Science, and Cell series
• Filters all papers through genomics keyword matching on title + abstract
• Deduplicates by DOI
• Fallback: If network is restricted (e.g., sandboxed environments), uses Claude's built-in WebSearch/WebFetch tools

Step 3: Download PDFs

• Attempts to download the full PDF for each paper
• bioRxiv: Uses the direct PDF URL pattern (/content/{doi}v{version}.full.pdf)
• Journals: Attempts PDF via Unpaywall API (free/legal open-access PDFs) and direct links
• Falls back to abstract-only review if PDF is unavailable

Step 4: Claude Reads PDFs and Reviews

• Claude reads each PDF (or abstract if PDF unavailable) natively
• Acts as a critical reviewer and assesses each paper on:
  • Novelty: How original and new is the contribution?
  • Rigor: Are the experiments well-designed and controls appropriate?
  • Methods: Are the methods appropriate, well-described, and reproducible?
  • Main Results: What are the key findings? Are they well-supported?
  • Limitations: What are the weaknesses and caveats?
  • Inspiration for the Field: What new directions does this work open?
  • Reviewer's Own Thoughts: Additional perspective and commentary

Step 5: Score the Manuscript

Each paper is scored on a 0-10 scale (with decimal precision, e.g., 5.1, 6.7):

Dimension	What it measures
Originality	Novelty of the question, approach, or finding
Methodology	Rigor, appropriateness, reproducibility of methods
Significance	Impact on the field and broader implications
Overall	Holistic assessment weighing all dimensions

Score guide:

• 9.0-10.0: Exceptional / groundbreaking
• 7.0-8.9: Strong contribution
• 5.0-6.9: Adequate but incremental
• 3.0-4.9: Significant concerns
• 0.0-2.9: Major flaws

Step 6: Generate Report

• Writes a detailed HTML review per paper in reviews/ with styled formatting
• Writes a summary HTML report ranking all papers by overall score

Features to add

• Let the model read abstract and discussion first, do an initial score of the paper. Then proceed to comprehensive review if it passed certain criteria.

Prerequisites