Bio Causal Genomics Mediation Analysis
GPTomics/bioSkills
Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML.
Develop theoretically grounded hypotheses and draft publication-ready Theory sections.
Install Scholar Hypothesis
$ npx skills add joshzyj/open-scholar-skill --skill scholar-hypothesis -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install joshzyj/open-scholar-skill scholar-hypothesis --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/joshzyj/open-scholar-skill.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/scholar-hypothesis .claude/skills/scholar-hypothesis && 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 "scholar-hypothesis" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-hypothesis into .claude/skills/scholar-hypothesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-hypothesis", 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/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-hypothesisType 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 joshzyj/open-scholar-skill --skill scholar-hypothesis -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install joshzyj/open-scholar-skill scholar-hypothesis --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.claude/skills/scholar-hypothesis .agents/skills/scholar-hypothesis && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "scholar-hypothesis" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-hypothesis into .agents/skills/scholar-hypothesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-hypothesis", 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 joshzyj/open-scholar-skill --skill scholar-hypothesis -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install joshzyj/open-scholar-skill scholar-hypothesis --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.claude/skills/scholar-hypothesis .cursor/skills/scholar-hypothesis && 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 "scholar-hypothesis" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-hypothesis into .cursor/skills/scholar-hypothesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-hypothesis", 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/joshzyj/open-scholar-skill.git --path .claude/skills/scholar-hypothesis--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 joshzyj/open-scholar-skill --skill scholar-hypothesis -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install joshzyj/open-scholar-skill scholar-hypothesis --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.claude/skills/scholar-hypothesis .gemini/skills/scholar-hypothesis && 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 "scholar-hypothesis" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-hypothesis into .gemini/skills/scholar-hypothesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-hypothesis", 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 joshzyj/open-scholar-skill scholar-hypothesisInstalls 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 joshzyj/open-scholar-skill --skill scholar-hypothesis -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .github/skills && cp -r skills-src/.claude/skills/scholar-hypothesis .github/skills/scholar-hypothesis && 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 "scholar-hypothesis" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-hypothesis into .github/skills/scholar-hypothesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-hypothesis", 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 joshzyj/open-scholar-skill --skill scholar-hypothesis -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install joshzyj/open-scholar-skill scholar-hypothesis --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/joshzyj/open-scholar-skill.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.claude/skills/scholar-hypothesis .opencode/skills/scholar-hypothesis && 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 "scholar-hypothesis" agent skill from https://github.com/joshzyj/open-scholar-skill/tree/main/.claude/skills/scholar-hypothesis into .opencode/skills/scholar-hypothesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scholar-hypothesis", 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
scholar-hypothesis- GitHub stars
- 168
- Token cost
- ~11k tokens
- SKILL.md length
- 3,452 words
- Files
- 2 (incl. references)
- Skills in repo
- 30
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Develop theoretically grounded hypotheses and draft publication-ready Theory sections.
- Works in 9 steps: Dispatch → Frame the Explanatory Puzzle → Select Theoretical Framework(s) → …
- Tasks that involve Speech recognition and synthesis
- SKILL.md covers Arguments, Step 0: Dispatch, Step 1: Frame the Explanatory… and Step 2: Select Theoretical…, plus 7 more sections
- Calls bash
What it does
Scholar Hypothesis is an agent skill from joshzyj/open-scholar-skill. Develop theoretically grounded hypotheses and draft publication-ready Theory sections. Covers puzzle framing (5 types: anomaly, contradiction, extension, mechanism, scope), framework selection from 25+ sociological/linguistic theories (stratification, networks, culture, institutional, life course, analytical sociology via Coleman's boat + Hedström DBO, intersectionality, racial formation, social movements, status characteristics, signaling, non-Western: guanxi/Ubuntu/coloniality/world-systems), mechanism chain…
Its SKILL.md is about 11k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including reference files (for example `references/theory-frameworks.md`).
It sits in AI & LLM Engineering, covering Speech recognition and synthesis and Dispute resolution. The repository describes itself as: Open scholar skill, a claude code plugin, for academic research.
When your agent uses it
- Tasks that involve Speech recognition and synthesis
- Tasks that involve Dispute resolution
Example prompts
- “/scholar-hypothesis”
Workflow steps
9 steps, taken from the step headings in SKILL.md.
- Dispatch
- Frame the Explanatory Puzzle
- Select Theoretical Framework(s)
- Specify the Mechanism Chain
- Derive and Formalize Hypotheses
- Map Competing Predictions
- Build the Text-Based DAG / Causal Graph
- Write the Theory Section
- Save Output
What it can do on your machine
Read from SKILL.md and the folder at commit 6e5ac8e. 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
Shell commands in SKILL.md call:
bash
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
Scholar Hypothesis loads about 11k tokens when it runs, and up to ~23k if it reads all its reference files. Until then it costs about 260 tokens; SKILL.md has 3,452 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); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 3,452 words (~11,041 tokens).
“You are an expert sociologist helping develop theoretically grounded, testable hypotheses and theory sections for publication-quality papers. Your output must meet the standards of ASR, AJS, Demography, Nature Human Behaviour, Science Advances, or Nature Computational Science.”
- name
- scholar-hypothesis
- tools
- Write, Bash, WebSearch, Read
- argument-hint
- [phenomenon or RQ] — optionally: [design type: quant/qual/comp/computational] [journal: ASR/AJS/Demography/NHB/NCS/SciAdv] [theory hint]
- user-invocable
- true
Files
SKILL.md and 1 other file (references) in .claude/skills/scholar-hypothesis of joshzyj/open-scholar-skill.
- SKILL.md
- references/theory-frameworks.md
Open the folder on GitHubat commit 6e5ac8e
Compare with similar skills
Scholar Hypothesis 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 |
|---|---|---|---|---|---|---|
| Scholar Hypothesis this skilljoshzyj/open-scholar-skill | 168 | — | ~11k | Automated safety check: Pass | Custom licence | |
| Bio Causal Genomics Mediation AnalysisGPTomics/bioSkills | 1.2k | 2 repos | ~8.6k | Automated safety check: Pass | MIT | |
| Bio Causal Genomics Mediation Analysisaipoch/medical-research-skills | 2k | 1 repos | ~2.6k | Automated safety check: Pass | MIT | |
| Multi AI Researchmajiayu000/spellbook | 287 | — | ~2k | Automated safety check: Pass | MIT | |
| Asr Literature Positioningfranklee16/academic-research-skills | 223 | 1 repos | ~798 | Automated safety check: Pass | None | |
| Jcr Tables Figuresfranklee16/academic-research-skills | 223 | 1 repos | ~1.1k | Automated safety check: Pass | None |
Similar skills
Bio Causal Genomics Mediation Analysis
aipoch/medical-research-skills
Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package.
Multi AI Research
majiayu000/spellbook
Parallel multi-AI cross-validation research workflow (大版本). An agent skill from majiayu000/spellbook.
Asr Literature Positioning
franklee16/academic-research-skills
A skill your agent uses when positioning an American Sociological Review (ASR) manuscript against the literature so it reads as a broad sociological contribution rather than a subfield note.
Jcr Tables Figures
franklee16/academic-research-skills
A skill your agent uses when building the exhibits for a Journal of Consumer Research (JCR) manuscript — study-summary tables, mediation/moderation results, interaction and spotlight plots…
Whisper Speech Recognition
Orchestra-Research/AI-Research-SKILLs
Transcribes audio with OpenAI's Whisper: 99 languages, translation to English, language detection, six model sizes and word-level timestamps, from Python or the CLI.
More from joshzyj/open-scholar-skill
All 30 skills in this repoScholar Annotate
joshzyj/open-scholar-skill
Turn unstructured text into validated, structured variables at corpus scale with LLMs: codebook design, dev/gold-set construction, DSPy prompt optimization, a hard reliability gate (Cohen κ ≥ 0.70)…
Scholar Auto Research
joshzyj/open-scholar-skill
Stable, deterministic social-science research-paper pipeline from idea or data to verified manuscript, citations, replication package, and final md/docx/tex/pdf outputs.
Scholar RAG
joshzyj/open-scholar-skill
Build and query a local vector database + GraphRAG over your entire reference library (Zotero or a PDF folder) for literature review.
Scholar Causal
joshzyj/open-scholar-skill
Comprehensive causal inference toolkit for social science research.
Scholar Data
joshzyj/open-scholar-skill
Comprehensive open data directory (100+ datasets across 14 categories) with auto-fetch capability, plus data collection instrument design, variable dictionaries, data management, IRB materials, and…
Scholar Eda
joshzyj/open-scholar-skill
Conduct exploratory data analysis (EDA) before hypothesis testing.
Related
Questions about Scholar Hypothesis
What does Scholar Hypothesis do?
Develop theoretically grounded hypotheses and draft publication-ready Theory sections. Scholar Hypothesis is an agent skill from joshzyj/open-scholar-skill. Develop theoretically grounded hypotheses and draft publication-ready Theory sections.
When should I use Scholar Hypothesis?
Scholar Hypothesis fits situations like: tasks that involve Speech recognition and synthesis; tasks that involve Dispute resolution.
How do I install Scholar Hypothesis in Claude Code?
Run `npx skills add joshzyj/open-scholar-skill --skill scholar-hypothesis -a claude-code`. Or copy the skill folder (.claude/skills/scholar-hypothesis in joshzyj/open-scholar-skill) into .claude/skills/scholar-hypothesis in your project. Claude Code loads it when a task matches its description.
How do I install Scholar Hypothesis in Codex?
Run `npx skills add joshzyj/open-scholar-skill --skill scholar-hypothesis -a codex`. Or copy the skill folder (.claude/skills/scholar-hypothesis in joshzyj/open-scholar-skill) into .agents/skills/scholar-hypothesis in your project. Codex loads it when a task matches its description.
Can I use Scholar Hypothesis 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 joshzyj/open-scholar-skill --skill scholar-hypothesis -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/scholar-hypothesis, .gemini/skills/scholar-hypothesis, .github/skills/scholar-hypothesis and .opencode/skills/scholar-hypothesis in your project.
What does Scholar Hypothesis need to run?
Going by SKILL.md and its folder, Scholar Hypothesis needs the command-line tools its instructions call (bash).
Does Scholar Hypothesis 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 Scholar Hypothesis 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. Review the folder before installing.
What licence does Scholar Hypothesis use?
Scholar Hypothesis has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Scholar Hypothesis use?
About 11k tokens (SKILL.md is roughly 44k 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 12k tokens, read only when the agent opens those files.
What are the alternatives to Scholar Hypothesis?
Skills that share tags, products or a category with Scholar Hypothesis: Bio Causal Genomics Mediation Analysis (GPTomics/bioSkills, 1.2k stars), Bio Causal Genomics Mediation Analysis (aipoch/medical-research-skills, 2k stars), Multi AI Research (majiayu000/spellbook, 287 stars) and Asr Literature Positioning (franklee16/academic-research-skills, 223 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Scholar Hypothesis?
joshzyj (a GitHub user) maintains it in joshzyj/open-scholar-skill, which has 168 GitHub stars. The repository holds 30 skills in this directory. The repository was last updated on September 18, 2026.
Source: joshzyj/open-scholar-skill on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.