GitHub Deep Research
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Guide agents through structured research including planning, multi-query execution, source analysis, and synthesis.
$ npx skills add jwynia/agent-skills --skill research-workflow -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install jwynia/agent-skills research-workflow --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/jwynia/agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/general/research/methodology/research-workflow .claude/skills/research-workflow && 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 "research-workflow" agent skill from https://github.com/jwynia/agent-skills/tree/main/skills/general/research/methodology/research-workflow into .claude/skills/research-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-workflow", 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/jwynia/agent-skills/tree/main/skills/general/research/methodology/research-workflowType 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 jwynia/agent-skills --skill research-workflow -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install jwynia/agent-skills research-workflow --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jwynia/agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/general/research/methodology/research-workflow .agents/skills/research-workflow && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "research-workflow" agent skill from https://github.com/jwynia/agent-skills/tree/main/skills/general/research/methodology/research-workflow into .agents/skills/research-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-workflow", 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 jwynia/agent-skills --skill research-workflow -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install jwynia/agent-skills research-workflow --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jwynia/agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/general/research/methodology/research-workflow .cursor/skills/research-workflow && 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 "research-workflow" agent skill from https://github.com/jwynia/agent-skills/tree/main/skills/general/research/methodology/research-workflow into .cursor/skills/research-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-workflow", 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/jwynia/agent-skills.git --path skills/general/research/methodology/research-workflow--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 jwynia/agent-skills --skill research-workflow -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install jwynia/agent-skills research-workflow --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jwynia/agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/general/research/methodology/research-workflow .gemini/skills/research-workflow && 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 "research-workflow" agent skill from https://github.com/jwynia/agent-skills/tree/main/skills/general/research/methodology/research-workflow into .gemini/skills/research-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-workflow", 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 jwynia/agent-skills research-workflowInstalls 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 jwynia/agent-skills --skill research-workflow -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/jwynia/agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/general/research/methodology/research-workflow .github/skills/research-workflow && 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 "research-workflow" agent skill from https://github.com/jwynia/agent-skills/tree/main/skills/general/research/methodology/research-workflow into .github/skills/research-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-workflow", 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 jwynia/agent-skills --skill research-workflow -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install jwynia/agent-skills research-workflow --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jwynia/agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/general/research/methodology/research-workflow .opencode/skills/research-workflow && 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 "research-workflow" agent skill from https://github.com/jwynia/agent-skills/tree/main/skills/general/research/methodology/research-workflow into .opencode/skills/research-workflow/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-workflow", 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.
research-workflowGuide agents through structured research including planning, multi-query execution, source analysis, and synthesis.
Research Workflow is an agent skill from jwynia/agent-skills. Guide agents through structured research including planning, multi-query execution, source analysis, and synthesis. Use for comprehensive topic research, deep investigation, or creating research reports. Keywords: research, investigate, deep dive, comprehensive, analysis, synthesis, report.
Its SKILL.md is about 2.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including reference files and assets (for example `assets/research-plan-template.md`, `assets/research-report-template.md` and `assets/source-evaluation-checklist.md`). Compatibility notes: Designed for Claude Code and similar products. Web search capability required.
It sits in Research & Science, covering Deep research. The licence is MIT.
4 steps, taken from the step headings in SKILL.md.
Read from SKILL.md and the folder at commit e02ec7e. It shows what the files ask for, not the result of running them.
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.
No scripts in the folder and no shell commands in SKILL.md (its code samples are bash).
From the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Designed for Claude Code and similar products. Web search capability required.
From compatibility in the SKILL.md frontmatter.
Research Workflow loads about 2.4k tokens when it runs, and up to ~4.9k if it reads all its reference files. Until then it costs about 77 tokens; SKILL.md has 714 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.
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); files beside SKILL.md are not scanned.
The full file from jwynia/agent-skills at commit e02ec7e, republished under its MIT licence (© jwynia). 714 words, ~2,442 tokens.
.claude/skills/research-workflow/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.A structured methodology for conducting comprehensive research. This skill guides you through planning, executing, analyzing, and synthesizing research on any topic.
Use this skill when:
Do NOT use this skill when:
Before using this skill, ensure:
┌─────────────────────────────────────────────────────────────┐
│ RESEARCH WORKFLOW │
├─────────────────────────────────────────────────────────────┤
│ │
│ 1. PLANNING 2. EXECUTION │
│ ┌──────────────┐ ┌──────────────┐ │
│ │ Define │ │ Run searches │ │
│ │ questions │───>│ Evaluate │ │
│ │ Plan queries │ │ sources │ │
│ └──────────────┘ └──────────────┘ │
│ │ │ │
│ v v │
│ 3. ANALYSIS 4. SYNTHESIS │
│ ┌──────────────┐ ┌──────────────┐ │
│ │ Organize │ │ Create │ │
│ │ findings │───>│ coherent │ │
│ │ Find patterns│ │ output │ │
│ └──────────────┘ └──────────────┘ │
│ │
└─────────────────────────────────────────────────────────────┘Before any searches, establish a clear research plan.
Convert the topic into specific, answerable questions.
Example:
Break down the main topic into searchable components:
Create a search plan with query progression:
Broad queries first: Get overall landscape
Specific queries next: Dive into details
Verification queries last: Confirm findings
Use the template at assets/research-plan-template.md to document your plan.
Execute your search plan systematically.
Execute queries in order, using appropriate search parameters:
# Broad overview
web-search "AI in healthcare overview 2024"
# Specific deep dive
web-search "AI diagnostic imaging applications" --depth advanced
# Current news
web-search "AI healthcare regulations 2024" --topic news --time monthFor each search, record:
Use the checklist at assets/source-evaluation-checklist.md to assess:
Credibility Indicators:
Quality Signals:
Research is not linear. Based on findings:
Organize and analyze your collected findings.
Organize results into categories:
Look for:
For each finding, determine confidence level:
Document:
Create coherent, useful output from your analysis.
Choose appropriate format based on use case:
Use the template at assets/research-report-template.md.
Key principles:
End with practical outputs:
Phase 1 - Planning:
Research Question: What are the best practices for API versioning?
Sub-questions:
1. What versioning strategies exist?
2. What are pros/cons of each?
3. What do major companies use?
4. What do experts recommend?
Search Plan:
- "API versioning strategies comparison"
- "REST API versioning best practices 2024"
- "API versioning header vs URL vs query parameter"
- "large companies API versioning approach"Phase 2 - Execution:
Query 1: "API versioning strategies comparison"
- Found: URL versioning, header versioning, query parameter
- Key insight: URL versioning most common, header more "RESTful"
- Sources: REST API tutorial, Martin Fowler blog
Query 2: "REST API versioning best practices 2024"
- Found: Semantic versioning principles apply
- Key insight: Version only when breaking changes
- Sources: API design guides, Stack Overflow discussionsPhase 3 - Analysis:
Consensus Points:
- Version only for breaking changes
- Be consistent within an API
- Document version lifecycle
Conflicts:
- URL vs header placement (no clear winner)
- When to deprecate old versions
Gaps:
- Limited data on performance impact
- Few studies on developer experiencePhase 4 - Synthesis:
Key Findings:
1. Three main strategies exist (URL, header, query param)
2. URL versioning is most common and discoverable
3. Header versioning is considered more "pure" REST
4. Version only on breaking changes
5. Major companies split between approaches
Recommendations:
- Use URL versioning for public APIs (discoverability)
- Consider header versioning for internal APIs
- Document deprecation timeline clearly
- Use semantic versioning principlesBefore completing research, verify:
For detailed guidance, see:
This workflow has the following limitations:
© jwynia, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 5 other files (references, assets) in skills/general/research/methodology/research-workflow of jwynia/agent-skills.
Open the folder on GitHubat commit e02ec7e
Research Workflow 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 |
|---|---|---|---|---|---|---|
| Research Workflow this skilljwynia/agent-skills | 169 | — | ~2.4k | Automated safety check: Pass | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 84k | 4 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Deep Research WorkflowTokenRhythm/opensquilla | 7.1k | — | ~1.3k | Automated safety check: Pass | Apache-2.0 | |
| Deep Researchsanjay3290/ai-skills | 431 | 9 repos | ~683 | Automated safety check: Notes | Apache-2.0 | |
| Horizontal-Vertical Deep ResearchKKKKhazix/khazix-skills | 21k | — | ~2.1k | Automated safety check: Pass | MIT | |
| Academic Research PipelineImbad0202/academic-research-skills | 51k | — | ~15k | Automated safety check: Pass | Custom licence |
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
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.
sanjay3290/ai-skills
Execute autonomous multi-step research using Google Gemini Deep Research Agent.
KKKKhazix/khazix-skills
Runs a two-axis deep research method on a product, company, concept or person: its full history over time, compared with peers today, delivered as a typeset PDF report.
Imbad0202/academic-research-skills
Orchestrates a ten-stage academic workflow from research to finished manuscript, including integrity checks, two rounds of peer review and revision.
Imbad0202/academic-research-skills-codex
A router skill that sends academic work such as literature reviews, drafting, citation checks, peer review and revision to the right workflow in the ARS suite.
jwynia/agent-skills
Diagnose devcontainer configuration problems and guide development environment setup.
jwynia/agent-skills
Create distinctive, production-grade frontend interfaces with high design quality.
jwynia/agent-skills
Orchestrate agile development workflows for Gitea repositories using the tea CLI.
jwynia/agent-skills
Generate game assets using AI image generation APIs (DALL-E, Replicate, fal.ai) and prepare them for Godot.
jwynia/agent-skills
Develop AI agents, tools, and workflows with Mastra v1 Beta and Hono servers.
jwynia/agent-skills
Create and manipulate PowerPoint PPTX files programmatically.
Categories
Guide agents through structured research including planning, multi-query execution, source analysis, and synthesis. Research Workflow is an agent skill from jwynia/agent-skills. Guide agents through structured research including planning, multi-query execution, source analysis, and synthesis.
Research Workflow fits situations like: comprehensive topic research; deep investigation; creating research reports.
Run `npx skills add jwynia/agent-skills --skill research-workflow -a claude-code`. Or copy the skill folder (skills/general/research/methodology/research-workflow in jwynia/agent-skills) into .claude/skills/research-workflow in your project. Claude Code loads it when a task matches its description.
Run `npx skills add jwynia/agent-skills --skill research-workflow -a codex`. Or copy the skill folder (skills/general/research/methodology/research-workflow in jwynia/agent-skills) into .agents/skills/research-workflow in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add jwynia/agent-skills --skill research-workflow -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/research-workflow, .gemini/skills/research-workflow, .github/skills/research-workflow and .opencode/skills/research-workflow in your project.
SKILL.md names no scripts, command-line tools or credentials: Research Workflow is instructions for the agent only. Compatibility (from SKILL.md): Designed for Claude Code and similar products. Web search capability required..
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.
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. Review the folder before installing.
Research Workflow is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.4k tokens (SKILL.md is roughly 9.8k 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 2.4k tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Research Workflow: GitHub Deep Research (bytedance/deer-flow, 84k stars), Deep Research Workflow (TokenRhythm/opensquilla, 7.1k stars), Deep Research (sanjay3290/ai-skills, 431 stars) and Horizontal-Vertical Deep Research (KKKKhazix/khazix-skills, 21k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
jwynia (a GitHub user) maintains it in jwynia/agent-skills, which has 169 GitHub stars. The repository holds 111 skills in this directory. The repository was last updated on February 24, 2026.
Source: jwynia/agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.