Skip to main content
affpapa.org
RU EN
skill CX Codex

deep-research · lingzhi227 — Claude Code skill: 6-phase literature reviews

Runs a systematic academic literature review on a topic: finds papers, reads them, builds a database and writes a final report. Useful when you need the state of a field, not a few search hits.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add lingzhi227/agent-research-skills --skill deep-research -a claude-code
Open on GitHub

What deep-research does

The skill works through six phases in strict order: latest conference material, a broad survey of the topic, deep reading of selected papers, a hunt for code and tools, synthesis with research gaps, and the final report. Skipping ahead is not allowed. Before each next phase the agent checks that the previous phase's files exist on disk and prints a completion checkpoint.

A set of scripts does the heavy lifting. paper_finder.py searches published conference papers with venue and year filters, search_semantic_scholar.py and search_arxiv.py add citation data and recent preprints, paper_db.py merges results into one database, extract_pdf.py pulls text out of PDFs, and compile_report.py assembles the report. Semantic Scholar needs an API key. Without Bash the skill falls back to WebSearch and WebFetch.

Peer-reviewed conference papers come first; preprints are supplementary and get marked as such in citations. So on a very fresh topic your pool will be thinner. Output lands in a topic folder split by phase, which means you can edit the intermediate notes by hand between runs.

What it helps with

  • map the state of a field from recent conference papers
  • build a paper database with BibTeX and citation counts
  • read the shortlisted papers and write notes on each
  • find open-source implementations and tools for the topic
  • spell out research gaps and write the final report

Example prompts for the agent

  • do a literature review on long horizon reasoning agents
  • /research retrieval augmented generation
  • deep dive into memory for LLM agents

How to install deep-research

1Skills CLI (Vercel)

npx skills add lingzhi227/agent-research-skills --skill deep-research -a claude-code

2Manually: put the files in place

~/.claude/skills/deep-research/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/deep-research/

Step by step, with commands for each platform: How to install skills in Claude Code: five ways

Questions about deep-research

How do I install deep-research in Claude?

Run npx skills add lingzhi227/agent-research-skills --skill deep-research -a claude-code. The skill lands in ~/.claude/skills/deep-research/ with its scripts and definition.

What does deep-research do?

It runs an academic literature review in 6 phases: recent conference material, a broad survey, deep reading, a code search, synthesis and the final report. You get structured notes, a paper database and a compiled report.

Can the deep reading phase be skipped?

No. The skill requires the phases in strict order and checks for the previous phase's output files before moving on. Synthesis without actually reading the papers comes out shallow.

Similar skills

Everything for Science and research →

deep-research by other authors comes first.

deep-research affaan-m Turns a vague “research this” request into a cited report: sub-questions, 15–30 sources, an inline reference under each finding and a confidence level. CX Codex +1 5,100installs deep-research bytedance A skill for thorough web research using multi-angle analysis methodology. Use it instead of basic search when you need to understand a topic from all angles before writing content or tackling a complex question. CX Codex +1 2,800installs deep-research 199-biotechnologies Runs multi-stage research, checks claims against sources, and assembles structured reports. Use it for complex analysis and comparisons, not quick lookups. CX Codex +1 10,200installs deep-research ruvnet Orchestrates multi-phase research using web search, codebase analysis, and memory storage. It generates structured findings with evidence ratings for complex topics. CX Codex +1 893installs deep-research HKUSTDial Runs a topic investigation in the shape of a survey paper: pins the questions, searches from several angles, checks every reference and answers each question in the final report. Useful before you commit to a topic. CX Codex +1 496installs literature-review collaborative-deep-research Runs a systematic literature review on an academic topic: searches papers, triages results, reads key works and writes a themed report. CX Codex +1 732installs research-lit wanshuiyin Searches for papers on a topic, finds related work and summarizes the key ideas. Useful when you need a literature review without digging through arXiv by hand. CX Codex +1 614installs academic-deep-research kesslerio A skill that runs multi-step research: two search cycles per theme, an evidence hierarchy and APA 7 citations. Useful for literature reviews and competitive intelligence. CX Codex +1 560installs tooluniverse-literature-deep-research mims-harvard A skill for deep literature search across PubMed, EuropePMC and bioRxiv, with citation networks and evidence grading. Useful when you need a review with citations. CX Codex +1 664installs research-ideation Galaxy-Dawn Guides the research project kickoff by framing questions through 5W1H, mapping literature gaps, and organizing papers in Zotero. CX Codex +1 566installs systematic-literature-review bytedance A skill to automatically search and synthesize multiple papers by topic from arXiv. Collects research, extracts key findings, and outputs reports in APA, IEEE, or BibTeX format. CX Codex +1 2,500installs

From the same set23

math-reasoning Derives equations, writes proofs, formalizes research problems, and produces publication-ready LaTeX markup for research papers. CX Codex +1 2,200installs latex-formatting Sets up conference LaTeX templates, fixes formatting, and runs a pre-submission check. Handy when the deadline is close. CX Codex +1 2,200installs citation-management A skill that keeps citations in a LaTeX paper in order: harvests missing references via Semantic Scholar, validates cite keys against .bib, and formats the bibliography. CX Codex +1 2,100installs backward-traceability Connects every numeric value in a research PDF directly to the source code line that produced it. Helps verify data reproducibility across LaTeX documents. CX Codex +1 2,100installs research-planning Turns a topic or idea into a structured research plan: methodology, paper sections, dependency-ordered tasks and diagrams. CX Codex +1 1,800installs github-research Finds open-source repositories matching research topics, inspects their codebases, and produces an integration blueprint. Useful when tracking down implementations of algorithms. CX Codex +1 1,800installs paper-writing-section A skill that drafts or reworks a single section of an academic paper, from abstract to conclusion. Useful when the research is done but the prose is not. CX Codex +1 1,800installs novelty-assessment Runs a research idea through literature search and returns a verdict: novel or not. Useful before you commit to a direction. CX Codex +1 1,800installs

Project sponsors

Companies that keep this analytics open
Gold sponsor
Nutra.Club

Impressions, clicks and code copies — open statistics. We keep the numbers public for the same reason NeBlask itself is public. Become a sponsor