Deep Research Literature Survey
HKUSTDial/Supervisor-Skills
Runs a survey-grade literature investigation: fixes the research questions, searches from adversarial angles, verifies citations and writes an evidence-first report.
Conduct systematic academic literature reviews in 6 phases, producing structured notes, a curated paper database, and a synthesized final report.
Install Deep Research
$ npx skills add lingzhi227/agent-research-skills --skill deep-research -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install lingzhi227/agent-research-skills deep-research --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/deep-research .claude/skills/deep-research && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "deep-research" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/deep-research into .claude/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/lingzhi227/agent-research-skills/tree/main/skills/deep-researchType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add lingzhi227/agent-research-skills --skill deep-research -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install lingzhi227/agent-research-skills deep-research --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/deep-research .agents/skills/deep-research && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "deep-research" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/deep-research into .agents/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add lingzhi227/agent-research-skills --skill deep-research -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install lingzhi227/agent-research-skills deep-research --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/deep-research .cursor/skills/deep-research && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "deep-research" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/deep-research into .cursor/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/lingzhi227/agent-research-skills.git --path skills/deep-research--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add lingzhi227/agent-research-skills --skill deep-research -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install lingzhi227/agent-research-skills deep-research --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/deep-research .gemini/skills/deep-research && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "deep-research" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/deep-research into .gemini/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install lingzhi227/agent-research-skills deep-researchInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add lingzhi227/agent-research-skills --skill deep-research -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/deep-research .github/skills/deep-research && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "deep-research" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/deep-research into .github/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add lingzhi227/agent-research-skills --skill deep-research -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install lingzhi227/agent-research-skills deep-research --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/deep-research .opencode/skills/deep-research && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "deep-research" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/deep-research into .opencode/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
deep-research- GitHub stars
- 390
- Token cost
- ~2.9k tokens
- SKILL.md length
- 1,084 words
- Files
- 11 (incl. scripts, references)
- Skills in repo
- 31
- Repo updated
- First seen
- Licence
- None found
At a glance
Conduct systematic academic literature reviews in 6 phases, producing structured notes, a curated paper database, and a synthesized final report.
- Works in 9 steps: paper_finder (primary — conference… → search_semantic_scholar.py… → search_arxiv.py (supplementary — latest… → …
- Tasks that involve Deep research
- SKILL.md covers Trigger, Overview, CRITICAL: Strict Sequential… and Paper Quality Policy, plus 6 more sections
- Runs Python scripts from its folder; calls python
What it does
Deep Research is an agent skill from lingzhi227/agent-research-skills. Conduct systematic academic literature reviews in 6 phases, producing structured notes, a curated paper database, and a synthesized final report. Output is organized by phase for clarity.
Its SKILL.md is about 2.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 12 other files, including scripts and reference files (for example `references/api-reference.md`, `references/note-format.md` and `references/workflow-phases.md`).
It sits in Research & Science, covering Deep research, Literature review and Academic paper search. The repository describes itself as: Skills for Claude Code — deep-research: systematic academic literature review.
When your agent uses it
- Tasks that involve Deep research
- Tasks that involve Literature review
- Tasks that involve Academic paper search
Example prompts
- “/deep-research”
Requirements
- Python 3
Workflow steps
9 steps, taken from the step headings in SKILL.md.
- paper_finder (primary — conference papers only)
- search_semantic_scholar.py (supplementary — citation data + broader coverage)
- search_arxiv.py (supplementary — latest preprints)
- Frontier
- Survey
- Deep Dive ⚠️ DO NOT SKIP
- Code & Tools ⚠️ DO NOT SKIP
- Synthesis (REQUIRES Phase 3 + 4 complete)
- Compilation (REQUIRES Phase 1-5 complete)
What it can do on your machine
Read from SKILL.md and the folder at commit 9e6c085. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 7 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Deep Research loads about 2.9k tokens when it runs, and up to ~7.6k if it reads all its reference files. Until then it costs about 50 tokens; SKILL.md has 1,084 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 1,084 words (~2,894 tokens).
“Activate this skill when the user wants to:”
- name
- deep-research
- argument-hint
- topic
Files
SKILL.md and 10 other files (scripts, references) in skills/deep-research of lingzhi227/agent-research-skills.
- SKILL.md
- references/api-reference.md
- references/note-format.md
- references/workflow-phases.md
- scripts/bibtex_manager.py
- scripts/compile_report.py
- scripts/download_papers.py
- scripts/extract_pdf.py
- scripts/paper_db.py
- scripts/search_arxiv.py
- scripts/search_semantic_scholar.py
Open the folder on GitHubat commit 9e6c085
Compare with similar skills
Deep Research next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Deep Research this skilllingzhi227/agent-research-skills | 390 | — | ~2.9k | Automated safety check: Pass | None | |
| Deep Research Literature SurveyHKUSTDial/Supervisor-Skills | 8.8k | — | ~2.4k | Automated safety check: Pass | CC-BY-NC-SA-4.0 | |
| Deep Science WriterCYC2002tommy/Deep-Research-Agent | 311 | — | ~8.7k | Automated safety check: Warn | MIT | |
| Literature Reviewneflibata-feng/MyArxiv-Agent | 126 | 20 repos | ~5.9k | Automated safety check: Notes | MIT | |
| Preprint Search on bioRxivLigphiDonk/Oh-my--paper | 739 | 12 repos | ~3.7k | Automated safety check: Pass | MIT | |
| Deep Research WorkflowTokenRhythm/opensquilla | 7.1k | — | ~1.3k | Automated safety check: Pass | Apache-2.0 |
Similar skills
Deep Science Writer
CYC2002tommy/Deep-Research-Agent
End-to-end scientific research pipeline combining Exa Search, Playwright, deep-research, text-humanization, and iterative Remi peer review.
Literature Review
neflibata-feng/MyArxiv-Agent
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).
Preprint Search on bioRxiv
LigphiDonk/Oh-my--paper
Searches bioRxiv life sciences preprints by keyword, author, date range or category with a Python script, returning JSON metadata and optional PDF downloads.
Deep Research Workflow
TokenRhythm/opensquilla
Runs multi-round research in three stages with a persisted state file, evidence tracking and a long-form report with per-claim citations.
Deep Research
sanjay3290/ai-skills
Execute autonomous multi-step research using Google Gemini Deep Research Agent.
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Related
Categories
Questions about Deep Research
What does Deep Research do?
Conduct systematic academic literature reviews in 6 phases, producing structured notes, a curated paper database, and a synthesized final report. Deep Research is an agent skill from lingzhi227/agent-research-skills. Conduct systematic academic literature reviews in 6 phases, producing structured notes, a curated paper database, and a synthesized final report.
When should I use Deep Research?
Deep Research fits situations like: tasks that involve Deep research; tasks that involve Literature review; tasks that involve Academic paper search.
How do I install Deep Research in Claude Code?
Run `npx skills add lingzhi227/agent-research-skills --skill deep-research -a claude-code`. Or copy the skill folder (skills/deep-research in lingzhi227/agent-research-skills) into .claude/skills/deep-research in your project. Claude Code loads it when a task matches its description.
How do I install Deep Research in Codex?
Run `npx skills add lingzhi227/agent-research-skills --skill deep-research -a codex`. Or copy the skill folder (skills/deep-research in lingzhi227/agent-research-skills) into .agents/skills/deep-research in your project. Codex loads it when a task matches its description.
Can I use Deep Research in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add lingzhi227/agent-research-skills --skill deep-research -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/deep-research, .gemini/skills/deep-research, .github/skills/deep-research and .opencode/skills/deep-research in your project.
What does Deep Research need to run?
Going by SKILL.md and its folder, Deep Research needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Deep Research access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Deep Research safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Deep Research use?
No licence was found for Deep Research or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Deep Research use?
About 2.9k tokens (SKILL.md is roughly 12k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 4.7k tokens, read only when the agent opens those files.
What are the alternatives to Deep Research?
Skills that share tags, products or a category with Deep Research: Deep Research Literature Survey (HKUSTDial/Supervisor-Skills, 8.8k stars), Deep Science Writer (CYC2002tommy/Deep-Research-Agent, 311 stars), Literature Review (neflibata-feng/MyArxiv-Agent, 126 stars) and Preprint Search on bioRxiv (LigphiDonk/Oh-my--paper, 739 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Deep Research?
lingzhi227 (a GitHub user) maintains it in lingzhi227/agent-research-skills, which has 390 GitHub stars. The repository holds 31 skills in this directory. The repository was last updated on February 27, 2026.
Source: lingzhi227/agent-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.