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.
Guides the user through an interactive conversation to define their research project, then generates researchbrief.json and tasks.json.
$ npx skills add LigphiDonk/Oh-my--paper --skill inno-pipeline-planner -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install LigphiDonk/Oh-my--paper inno-pipeline-planner --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/LigphiDonk/Oh-my--paper.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/inno-pipeline-planner .claude/skills/inno-pipeline-planner && 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 "inno-pipeline-planner" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/inno-pipeline-planner into .claude/skills/inno-pipeline-planner/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inno-pipeline-planner", 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/LigphiDonk/Oh-my--paper/tree/main/skills/inno-pipeline-plannerType 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 LigphiDonk/Oh-my--paper --skill inno-pipeline-planner -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install LigphiDonk/Oh-my--paper inno-pipeline-planner --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/LigphiDonk/Oh-my--paper.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/inno-pipeline-planner .agents/skills/inno-pipeline-planner && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "inno-pipeline-planner" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/inno-pipeline-planner into .agents/skills/inno-pipeline-planner/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inno-pipeline-planner", 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 LigphiDonk/Oh-my--paper --skill inno-pipeline-planner -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install LigphiDonk/Oh-my--paper inno-pipeline-planner --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/LigphiDonk/Oh-my--paper.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/inno-pipeline-planner .cursor/skills/inno-pipeline-planner && 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 "inno-pipeline-planner" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/inno-pipeline-planner into .cursor/skills/inno-pipeline-planner/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inno-pipeline-planner", 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/LigphiDonk/Oh-my--paper.git --path skills/inno-pipeline-planner--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 LigphiDonk/Oh-my--paper --skill inno-pipeline-planner -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install LigphiDonk/Oh-my--paper inno-pipeline-planner --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/LigphiDonk/Oh-my--paper.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/inno-pipeline-planner .gemini/skills/inno-pipeline-planner && 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 "inno-pipeline-planner" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/inno-pipeline-planner into .gemini/skills/inno-pipeline-planner/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inno-pipeline-planner", 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 LigphiDonk/Oh-my--paper inno-pipeline-plannerInstalls 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 LigphiDonk/Oh-my--paper --skill inno-pipeline-planner -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/LigphiDonk/Oh-my--paper.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/inno-pipeline-planner .github/skills/inno-pipeline-planner && 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 "inno-pipeline-planner" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/inno-pipeline-planner into .github/skills/inno-pipeline-planner/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inno-pipeline-planner", 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 LigphiDonk/Oh-my--paper --skill inno-pipeline-planner -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install LigphiDonk/Oh-my--paper inno-pipeline-planner --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/LigphiDonk/Oh-my--paper.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/inno-pipeline-planner .opencode/skills/inno-pipeline-planner && 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 "inno-pipeline-planner" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/inno-pipeline-planner into .opencode/skills/inno-pipeline-planner/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "inno-pipeline-planner", 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.
inno-pipeline-plannerGuides the user through an interactive conversation to define their research project, then generates researchbrief.json and tasks.json.
Inno Pipeline Planner is an agent skill from LigphiDonk/Oh-my--paper. Guides the user through an interactive conversation to define their research project, then generates researchbrief.json and tasks.json.
Its SKILL.md is about 1.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including reference files (for example `agents/openai.yaml`, `references/brief-schema.md` and `references/generation-rules.md`).
It sits in Research & Science, covering Deep research. The repository describes itself as: A Claude Code plugin that turns your terminal into an autonomous research lab — literature survey, experiment execution, paper writing, all in one pipeline. The licence is MIT.
5 steps, taken from the step headings in SKILL.md.
Read from SKILL.md and the folder at commit 6baece9. 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.
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.
Inno Pipeline Planner loads about 1.8k tokens when it runs, and up to ~4.9k if it reads all its reference files. Until then it costs about 40 tokens; SKILL.md has 721 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 LigphiDonk/Oh-my--paper at commit 6baece9, republished under its MIT licence (© LigphiDonk). 721 words, ~1,756 tokens.
.claude/skills/inno-pipeline-planner/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.Guides the user through an interactive conversation to define their research project, then generates research_brief.json and tasks.json. Use when starting a new project, when no research_brief.json exists, when the user wants to start from...
Use this skill when the user request matches its research workflow scope. Prefer the bundled resources instead of recreating templates or reference material. Keep outputs traceable to project files, citations, scripts, or upstream evidence.
references/ only when the current task needs the extra detail.Run an interactive planning flow that turns user conversation into:
.pipeline/docs/research_brief.json.pipeline/tasks/tasks.jsonKeep this file short. Load full schemas and field-level rules from:
references/pipeline-contract.md (index)Read only what you need:
references/generation-rules.md: generation logic, ordering, dependencies, nextActionPromptreferences/brief-schema.md: .pipeline/docs/research_brief.json contractreferences/tasks-schema.md: .pipeline/tasks/tasks.json contractCheck:
.pipeline/docs/research_brief.json.pipeline/tasks/tasks.jsoninstance.json (legacy source)Survey/, Ideation/, Experiment/, Publication/, and Promotion/ directories (to detect pre-existing artifacts)If brief exists, summarize title, goal, current startStage, and completion status, then ask:
Capture at least:
Determine the starting stage early in the conversation:
startStage = "survey"startStage = "experiment"startStage = "publication"startStage = "promotion"startStage = "survey" (default)Typical question buckets:
Adapt to context:
startStage: If starting from experiment, do not ask survey or ideation questions in detail — just capture a brief summary of the existing context in those sections.pipeline.mode = "plan"; otherwise use "idea".Create if missing:
.pipeline/config.json.pipeline/docs/research_brief.json.pipeline/tasks/tasks.jsonUse the exact JSON contracts and generation rules in:
references/pipeline-contract.md and linked reference filesRules:
pipeline.startStage to the determined starting stage (default: "survey").startStage in the stage order (survey < ideation < experiment < publication < promotion).sections.* fields in the brief with whatever context the user provided, but do not create task blueprints or tasks for them..agents/skills/ or skills/), optionally using stage-skill-map.json if present.After writing files, present:
If user asks for updates:
tasks.json when pipeline structure/blueprints/stages change.pipeline.startStage in the brief, then regenerate tasks.json to include only the active stages.id instead of full regeneration.© LigphiDonk, 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) in skills/inno-pipeline-planner of LigphiDonk/Oh-my--paper.
Open the folder on GitHubat commit 6baece9
Inno Pipeline Planner 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 |
|---|---|---|---|---|---|---|
| Inno Pipeline Planner this skillLigphiDonk/Oh-my--paper | 739 | — | ~1.8k | 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 | 432 | 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.
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.
LigphiDonk/Oh-my--paper
Searches and downloads legally accessible academic PDFs, OCRs them to Markdown, and organizes the results into a traceable, AI-readable literature library.
LigphiDonk/Oh-my--paper
Finds and clones missing code repositories for a chosen research idea, then writes a survey that maps academic concepts to their implementations.
LigphiDonk/Oh-my--paper
Turns experimental data such as CSV, JSON or TensorBoard logs into statistical significance tests, visualizations and a drafted Results section.
LigphiDonk/Oh-my--paper
Lays out principles for catching fake, mismatched, or inconsistently formatted citations in academic writing, checked through live web search.
LigphiDonk/Oh-my--paper
Runs a seven-step quality-control and exploration pipeline on scRNA-seq, CyTOF or flow cytometry data and writes a plain-language report of what it found.
Categories
Guides the user through an interactive conversation to define their research project, then generates researchbrief.json and tasks.json. Inno Pipeline Planner is an agent skill from LigphiDonk/Oh-my--paper.json.
Inno Pipeline Planner fits situations like: tasks that involve Deep research.
Run `npx skills add LigphiDonk/Oh-my--paper --skill inno-pipeline-planner -a claude-code`. Or copy the skill folder (skills/inno-pipeline-planner in LigphiDonk/Oh-my--paper) into .claude/skills/inno-pipeline-planner in your project. Claude Code loads it when a task matches its description.
Run `npx skills add LigphiDonk/Oh-my--paper --skill inno-pipeline-planner -a codex`. Or copy the skill folder (skills/inno-pipeline-planner in LigphiDonk/Oh-my--paper) into .agents/skills/inno-pipeline-planner 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 LigphiDonk/Oh-my--paper --skill inno-pipeline-planner -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/inno-pipeline-planner, .gemini/skills/inno-pipeline-planner, .github/skills/inno-pipeline-planner and .opencode/skills/inno-pipeline-planner in your project.
SKILL.md names no scripts, command-line tools or credentials: Inno Pipeline Planner is instructions for the agent only.
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.
Inno Pipeline Planner is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 1.8k tokens (SKILL.md is roughly 7k 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 3.1k tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Inno Pipeline Planner: GitHub Deep Research (bytedance/deer-flow, 84k stars), Deep Research Workflow (TokenRhythm/opensquilla, 7.1k stars), Deep Research (sanjay3290/ai-skills, 432 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.
LigphiDonk (a GitHub user) maintains it in LigphiDonk/Oh-my--paper, which has 739 GitHub stars. The repository holds 27 skills in this directory. The repository was last updated on April 15, 2026.
Source: LigphiDonk/Oh-my--paper on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.