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.
Academic research assistant for literature reviews, paper analysis, and scholarly writing.
$ npx skills add LigphiDonk/Oh-my--paper --skill academic-researcher -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install LigphiDonk/Oh-my--paper academic-researcher --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/academic-researcher .claude/skills/academic-researcher && 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 "academic-researcher" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/academic-researcher into .claude/skills/academic-researcher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "academic-researcher", 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/academic-researcherType 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 academic-researcher -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install LigphiDonk/Oh-my--paper academic-researcher --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/academic-researcher .agents/skills/academic-researcher && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "academic-researcher" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/academic-researcher into .agents/skills/academic-researcher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "academic-researcher", 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 academic-researcher -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install LigphiDonk/Oh-my--paper academic-researcher --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/academic-researcher .cursor/skills/academic-researcher && 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 "academic-researcher" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/academic-researcher into .cursor/skills/academic-researcher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "academic-researcher", 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/academic-researcher--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 academic-researcher -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install LigphiDonk/Oh-my--paper academic-researcher --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/academic-researcher .gemini/skills/academic-researcher && 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 "academic-researcher" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/academic-researcher into .gemini/skills/academic-researcher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "academic-researcher", 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 academic-researcherInstalls 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 academic-researcher -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/academic-researcher .github/skills/academic-researcher && 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 "academic-researcher" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/academic-researcher into .github/skills/academic-researcher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "academic-researcher", 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 academic-researcher -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 academic-researcher --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/academic-researcher .opencode/skills/academic-researcher && 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 "academic-researcher" agent skill from https://github.com/LigphiDonk/Oh-my--paper/tree/main/skills/academic-researcher into .opencode/skills/academic-researcher/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "academic-researcher", 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.
academic-researcherAcademic research assistant for literature reviews, paper analysis, and scholarly writing.
Academic Researcher is an agent skill from LigphiDonk/Oh-my--paper. Academic research assistant for literature reviews, paper analysis, and scholarly writing.
Its SKILL.md is about 2.5k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Literature review and 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 (its code samples are markdown).
From the folder's file list and the shell code blocks in SKILL.md.
Hosts in commands or code, which the agent is likely to contact:
doi.orgFrom 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.
Academic Researcher loads about 2.5k tokens when it runs. Until then it costs about 28 tokens; SKILL.md has 875 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). 875 words, ~2,545 tokens.
.claude/skills/academic-researcher/SKILL.md (or your agent's skills folder).Academic research assistant for literature reviews, paper analysis, and scholarly writing. Use when: reviewing academic papers, conducting literature reviews, writing research summaries, analyzing methodologies, formatting citations, or wh...
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.
You are an academic research assistant with expertise across disciplines for literature reviews, paper analysis, and scholarly writing.
Use this skill when:
When reviewing academic papers, address:
Journal article:
Author, A. A., & Author, B. B. (Year). Title of article. Title of Periodical, volume(issue), pages. https://doi.org/xxx
Book:
Author, A. A. (Year). Title of book (Edition). Publisher.Journal article:
Author Last Name, First Name. "Title of Article." Title of Journal, vol. #, no. #, Year, pages.
Book:
Author Last Name, First Name. Title of Book. Publisher, Year.Footnote:
1. First Name Last Name, "Title of Article," Title of Journal vol, no. # (Year): pages.
Bibliography:
Last Name, First Name. "Title of Article." Title of Journal vol, no. # (Year): pages.## Introduction
- Define the research question or topic
- Explain significance and scope
- Preview organization
## Theoretical Framework
- Key theories and concepts
- How they relate to the topic
## [Theme 1]
- Synthesize relevant studies
- Note patterns and trends
- Identify agreements and disagreements
## [Theme 2]
[Continue for each theme/subtopic]
## Research Gaps
- What's missing from current literature
- Limitations of existing studies
- Opportunities for future research
## Conclusion
- Summary of key insights
- Implications for theory and practice
## References
[Formatted citation list]For paper summaries:
## Citation
[Full formatted citation]
## Research Question
[What the study investigates]
## Methodology
- **Design**: [Experimental, survey, qualitative, etc.]
- **Participants/Data**: [Sample description]
- **Measures**: [Key variables and instruments]
- **Analysis**: [Statistical or analytical methods]
## Key Findings
1. [Main finding with brief explanation]
2. [Second finding]
3. [Additional findings]
## Significance
[Why this research matters]
## Limitations
- [Methodological limitation]
- [Generalizability concerns]
- [Other caveats]
## Future Directions
[Suggested areas for future research]
## Personal Notes
[Optional: Connections to other work, questions, critiques]User Request: "Summarize research on spaced repetition for learning"
Response:
Spaced repetition is a learning technique where review sessions are distributed over increasing time intervals. Extensive research demonstrates its superiority to massed practice (cramming) for long-term retention across diverse materials and populations.
Ebbinghaus (1885) - Original discovery
Cepeda et al. (2006) - Meta-analysis
Citation: Cepeda, N. J., Pashler, H., Vul, E., Wixted, J. T., & Rohrer, D. (2006). Distributed practice in verbal recall tasks: A review and quantitative synthesis. Psychological Bulletin, 132(3), 354-380. https://doi.org/10.1037/0033-2909.132.3.354
Karpicke & Roediger (2008) - Retrieval practice
Three proposed mechanisms:
Effective implementations:
Optimal scheduling:
Based on current evidence:
Note: Full citations in APA format
Cepeda, N. J., Pashler, H., Vul, E., Wixted, J. T., & Rohrer, D. (2006). Distributed practice in verbal recall tasks: A review and quantitative synthesis. Psychological Bulletin, 132(3), 354-380.
Karpicke, J. D., & Roediger, H. L. (2008). The critical importance of retrieval for learning. Science, 319(5865), 966-968.
Dunlosky, J., Rawson, K. A., Marsh, E. J., Nathan, M. J., & Willingham, D. T. (2013). Improving students' learning with effective learning techniques. Psychological Science in the Public Interest, 14(1), 4-58.
© LigphiDonk, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Just SKILL.md in skills/academic-researcher of LigphiDonk/Oh-my--paper.
Open the folder on GitHubat commit 6baece9
Academic Researcher 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 |
|---|---|---|---|---|---|---|
| Academic Researcher this skillLigphiDonk/Oh-my--paper | 739 | — | ~2.5k | 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 | |
| Academic Research PipelineImbad0202/academic-research-skills | 51k | — | ~15k | Automated safety check: Pass | Custom licence | |
| Academic Research Suite for CodexImbad0202/academic-research-skills-codex | 12k | — | ~12k | Automated safety check: Pass | Custom licence | |
| Deep Research Agent TeamImbad0202/academic-research-skills | 51k | — | ~13k | Automated safety check: Pass | Custom licence |
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.
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.
Imbad0202/academic-research-skills
Runs a 13-agent pipeline for rigorous academic research, from forming the question through systematic search, synthesis, bias checks and an APA 7.0 report.
delorenj/mcp-server-trello
Decision-grade research, three ways: draft a deep-research prompt for the user to run in their own tool (ChatGPT, Gemini, Grok, Perplexity, …), process a finished research report — file it, distill…
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
Academic research assistant for literature reviews, paper analysis, and scholarly writing. Academic Researcher is an agent skill from LigphiDonk/Oh-my--paper. Academic research assistant for literature reviews, paper analysis, and scholarly writing.
Academic Researcher fits situations like: tasks that involve Literature review; tasks that involve Deep research.
Run `npx skills add LigphiDonk/Oh-my--paper --skill academic-researcher -a claude-code`. Or copy the skill folder (skills/academic-researcher in LigphiDonk/Oh-my--paper) into .claude/skills/academic-researcher in your project. Claude Code loads it when a task matches its description.
Run `npx skills add LigphiDonk/Oh-my--paper --skill academic-researcher -a codex`. Or copy the skill folder (skills/academic-researcher in LigphiDonk/Oh-my--paper) into .agents/skills/academic-researcher 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 academic-researcher -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/academic-researcher, .gemini/skills/academic-researcher, .github/skills/academic-researcher and .opencode/skills/academic-researcher in your project.
SKILL.md names no scripts, command-line tools or credentials: Academic Researcher is instructions for the agent only.
SKILL.md names 1 domain. In commands or code: doi.org; the agent is likely to contact it when it follows the instructions. 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.
Academic Researcher is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.5k tokens (SKILL.md is roughly 10k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Academic Researcher: Deep Research Workflow (TokenRhythm/opensquilla, 7.1k stars), Deep Research (sanjay3290/ai-skills, 432 stars), Academic Research Pipeline (Imbad0202/academic-research-skills, 51k stars) and Academic Research Suite for Codex (Imbad0202/academic-research-skills-codex, 12k 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.