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deep-research

deep-research

github.com/collaborative-deep-researchProductivity50319 installsUpdated 32w ago
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About deep-research

deep-research is a research skill that uses the paper and paper-search CLI tools to discover, read, and synthesize academic and web sources. It is for researchers who need a structured literature review with findings, gaps, and citations.

Key features

  1. 01Search the web and academic papers broadly
  2. 02Filter papers by year and citations
  3. 03Outline, skim, and read selected papers
  4. 04Explore citations and references
  5. 05Synthesize findings with citations and BibTeX

Use cases

  1. 01Map research on a topic before reading deeply
  2. 02Compare agreement and disagreement across studies
  3. 03Identify gaps and document sources

Install

Copy the command and run it in a terminal.

$npx skills add https://github.com/collaborative-deep-research/agent-papers-cli --skill deep-research

After installing, type/deep-researchin Claude Code to confirm it loaded.

Details

From the project README

Research "$ARGUMENTS" in depth using the paper and paper-search CLI tools. Follow this workflow:

1. Broad Discovery

Start with broad searches to map the landscape:

paper-search google web "$ARGUMENTS"
paper-search semanticscholar papers "$ARGUMENTS" --limit 10

Scan titles, snippets, and citation counts. Identify the most relevant papers and key terms.

2. Narrow and Filter

Refine based on what you found:

paper-search semanticscholar papers "<refined query>" --year 2023-2025 --min-citations 10
paper-search semanticscholar snippets "<specific question>"
paper-search pubmed "<query>"   # if biomedical

3. Deep Read

For the most relevant papers (at least 3-5), read in depth:

paper outline <arxiv_id>           # understand structure first
paper skim <arxiv_id> --lines 3    # quick overview
paper read <arxiv_id> <section>    # read key sections

For web sources:

paper-search browse <url>

4. Follow the Citation Graph

For key papers, explore their context:

paper-search semanticscholar citations <paper_id> --limit 10    # who cites this?
paper-search semanticscholar references <paper_id> --limit 10   # what does it build on?
paper-search semanticscholar details <paper_id>                  # full metadata

5. Synthesize

Combine findings into a structured report with:

  • Key findings and themes
  • Areas of agreement/disagreement
  • Gaps in the literature
  • Citations for all claims (include paper titles and URLs)
  • BibTeX entries for key papers (use paper bibtex <arxiv_id> to generate)

Guidelines

  • Always start broad, then narrow. Don't read deeply until you've scanned widely.
  • Read at least 3-5 primary sources before synthesizing.
  • Cross-reference web sources against academic papers when possible.
  • Use paper-search semanticscholar snippets to find specific evidence for claims.
  • Track what you've already searched/read to avoid redundancy.
  • If a search returns arxiv papers, use paper read to get the full text rather than just the snippet.

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