Deep Research
- 296 installs
- 48 repo stars
- Updated March 22, 2026
- collaborative-deep-research/agent-papers-cli
Run a structured literature and web deep-dive with academic search, paper reading, and citation-graph traversal via the paper CLI.
About
Deep-research is an agent skill that walks a solo builder through systematic topic investigation using the paper and paper-search CLI tools. It starts with wide web and Semantics Scholar queries, then refines with year, citation, and domain filters (including PubMed when biomedical). For the strongest hits, the agent outlines, skims, and reads sections of papers, browses key URLs, and walks citations and references to build context. It fits indie builders who need evidence-backed answers before scoping a product, picking a stack, or writing a spec—not a quick single-query chat answer. The workflow is procedural and repeatable, so you can hand the same ritual to Claude Code, Cursor, or Codex whenever a question deserves primary sources and traceable citations rather than model recall alone.
- Four-step workflow: broad discovery, narrow/filter, deep read (3–5 papers), citation graph exploration
- Semantics Scholar, Google web, PubMed, and browse commands for landscape mapping and snippets
- Paper CLI depth: outline, skim, and section reads for arXiv-style sources
- Citation and reference queries to surface influential prior and follow-on work
- Allowed agent tools: Bash, Read, Glob, Grep, Write for CLI-driven research sessions
Deep Research by the numbers
- 296 all-time installs (skills.sh)
- Ranked #592 of 2,064 Data Science & ML skills by installs in the Skillselion catalog
- Security screen: MEDIUM risk (skills.sh audit)
- Data as of Jul 29, 2026 (Skillselion catalog sync)
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| Installs | 296 |
|---|---|
| repo stars | ★ 48 |
| Security audit | 2 / 3 scanners passed |
| Last updated | March 22, 2026 |
| Repository | collaborative-deep-research/agent-papers-cli ↗ |
What it does
Run a structured literature and web deep-dive with academic search, paper reading, and citation-graph traversal via the paper CLI.
Files
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 10Scan 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 biomedical3. 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 sectionsFor 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 metadata5. 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 snippetsto find specific evidence for claims. - Track what you've already searched/read to avoid redundancy.
- If a search returns arxiv papers, use
paper readto get the full text rather than just the snippet.
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Is Deep Research safe to install?
skills.sh reports 2 of 3 security scanners passed. Review the Security Audits panel on this page before installing in production.