Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
A skill your agent uses when turning a personal agent skill into an open-source, distributable one.
$ npx skills add Aperivue/medsci-skills --skill publish-skill -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install Aperivue/medsci-skills publish-skill --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/Aperivue/medsci-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/publish-skill .claude/skills/publish-skill && 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 "publish-skill" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/publish-skill into .claude/skills/publish-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "publish-skill", 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/Aperivue/medsci-skills/tree/main/skills/publish-skillType 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 Aperivue/medsci-skills --skill publish-skill -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install Aperivue/medsci-skills publish-skill --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/publish-skill .agents/skills/publish-skill && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "publish-skill" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/publish-skill into .agents/skills/publish-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "publish-skill", 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 Aperivue/medsci-skills --skill publish-skill -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install Aperivue/medsci-skills publish-skill --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/publish-skill .cursor/skills/publish-skill && 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 "publish-skill" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/publish-skill into .cursor/skills/publish-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "publish-skill", 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/Aperivue/medsci-skills.git --path skills/publish-skill--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 Aperivue/medsci-skills --skill publish-skill -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install Aperivue/medsci-skills publish-skill --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/publish-skill .gemini/skills/publish-skill && 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 "publish-skill" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/publish-skill into .gemini/skills/publish-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "publish-skill", 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 Aperivue/medsci-skills publish-skillInstalls 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 Aperivue/medsci-skills --skill publish-skill -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/publish-skill .github/skills/publish-skill && 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 "publish-skill" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/publish-skill into .github/skills/publish-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "publish-skill", 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 Aperivue/medsci-skills --skill publish-skill -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install Aperivue/medsci-skills publish-skill --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Aperivue/medsci-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/publish-skill .opencode/skills/publish-skill && 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 "publish-skill" agent skill from https://github.com/Aperivue/medsci-skills/tree/main/skills/publish-skill into .opencode/skills/publish-skill/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "publish-skill", 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.
publish-skillA skill your agent uses when turning a personal agent skill into an open-source, distributable one.
Publish Skill is an agent skill from Aperivue/medsci-skills. Use when turning a personal agent skill into an open-source, distributable one. Runs a PII audit, generalizes personal details, checks licence compatibility, reviews cross-platform adapters and walks through packaging.
Its SKILL.md is about 3.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 9 other files, including scripts and reference files (for example `references/classroom-distribution.md`, `references/license-compatibility-matrix.md` and `references/pii-patterns.md`).
It sits in Research & Science. The repository describes itself as: Agent Skills for medical research — literature search, reporting-guideline & citation checks, statistics, publication figures, submission. Works with Claude Code, Codex, Cursor &… The licence is MIT.
8 steps, taken from the step headings in SKILL.md.
Read from SKILL.md and the folder at commit 3b14ae2. 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.
Ships 1 file in scripts/ (Shell), which the agent can run.
Shell commands in SKILL.md call:
gitbashFrom the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md. Its commands use git, which can reach the network depending on how they are called.
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.
Publish Skill loads about 3.2k tokens when it runs, and up to ~5.5k if it reads all its reference files. Until then it costs about 58 tokens; SKILL.md has 1,528 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); the scripts in this folder are not scanned.
The full file from Aperivue/medsci-skills at commit 3b14ae2, republished under its MIT licence (© Aperivue). 1,528 words, ~3,216 tokens.
.claude/skills/publish-skill/SKILL.md (or your agent's skills folder). This skill also uses 6 other files; get the full folder from GitHub.Collect from the user:
~/.claude/skills/my-skill/ or ~/.agents/skills/my-skill/)~/workspace/<your-package>/)SKILL.md from the source skill directoryls -R)| File | Lines | Type | Notes |
|------|-------|------|-------|Make every later fix on a working copy (<cleaned_skill_path> below) or in the target directory.
NEVER modify the source skill in place, because it is the user's working original.
Gate: User confirms source skill and target package before proceeding.
Before spending effort on PII scrubbing and generalization, confirm the workflow is worth distributing as a skill at all. Apply all three gates:
| Gate | Question | Pass condition |
|---|---|---|
| Uniqueness | Could a competent user get the same result by searching the web for ~5 minutes, or by asking a general assistant with no skill installed? | No |
| Specificity | Does it encode a workflow, decision heuristic, constraint, or convention specific to this domain or a recurring task — rather than a generic code snippet or a standard-library example? | Yes |
| Effort | Did discovering it take real debugging, study design, operational effort, or a reviewer-anticipation lesson (a pitfall, a verification step, a domain convention)? | Yes |
Gate: Any "no" (or "yes" on the inverse) stops publication — recommend documentation or a memory note instead. If the value is real but the skill delegates to private agents, route through Phase 1's orchestrator finding (refactor to standalone first). Only a clear three-way pass proceeds.
references/ come from external sources (published guidelines, textbooks, standards bodies)?| Finding | Action |
|---|---|
| Fully original | Proceed to Phase 2 |
| Adapted with compatible license | Add attribution header, proceed |
| Contains non-compatible third-party content | Flag for removal or URL reference conversion |
| Orchestrator with private agent references | STOP -- requires refactoring to standalone first |
| Competitive/proprietary logic | STOP -- not suitable for open-source |
Zero tolerance: the skill must have exactly 0 PII matches before proceeding.
Before running, ask the user for everything unique to them that should also count as a PII hit:
<First Last>|<native-script name>)<Institution>|<Hospital>)Combine the inputs into a single grep -E alternation pattern (pipe-separated).
Run the bundled audit script. The first argument is the skill directory; the second is the user-specific alternation pattern from Pre-scan Setup.
bash ${CLAUDE_SKILL_DIR}/scripts/audit_skill.sh --strict <source_skill_path> \
"<First Last>|<native-script name>|<Institution>|<Hospital>"The script scans ten categories, plus the user pattern:
/Users/<name>/, /home/<name>/, ~/Documents, ~/Desktop, ~/Downloads, ~/Projects)*.internal, *.local, *.corp)professor <Surname>, Prof. <Surname>, Dr. <Surname>, PGY[0-9], <한글이름> 교수님)> YYYY-MM-DD ... lines that reveal an internal review timeline)<Surname>{Year}_* pattern, e.g., <Surname>2025_<Journal>_Fig01.png; allow-list excludes generic tokens like Issue2024_, Sample2025_)exiftool for home paths, email addresses and the user pattern, matched case-insensitively. If binaries are present and exiftool is not installed, the RESULT line reads INCOMPLETE and --strict exits 3)Exit codes: 0 clean, 1 findings, 2 usage error / invalid user regex / a scan that could not run, 3 (--strict only) a check that could not run. Only exit 0 means clean.
Known limits: the Korean role branch (item 5) requires the honorific -nim suffix. A bare third-person mention (a Korean name followed by the role word without -nim) is not caught by this script, because separating it from job descriptions such as "advising professor" needs a stoplist that grep -E cannot express. Check such mentions by hand.
For categories the script flags, also verify manually with the Grep tool against ${CLAUDE_SKILL_DIR}/references/pii-patterns.md. Pay particular attention to:
CK-NN, MA-NN, dated cohort namesPresent all findings in a remediation table:
| # | File:Line | Category | Match | Suggested Fix |
|---|-----------|----------|-------|---------------|Gate: User reviews all findings. Fix each one in the working copy. Re-run the audit on the working copy. Proceed only when 0 hits are confirmed.
"in Korean" / "한국어로" / "Korean language" → "in the user's preferred language""communicate in [specific language]" → "Communicate with the user in their preferred language"metadata.triggers field (or the target package's equivalent) (these aid discovery)"radiology researcher" → "medical researcher" (if the skill is domain-general)"professor" / "fellow" → "researcher" or "user" (context-dependent)${CLAUDE_SKILL_DIR} for bundled reference files~/Documents/... → user-provided output directorytools: field, and allowed-tools pre-approves tools rather than describing them, so do not move requirements thereanalyze-stats")?Show a unified diff of all generalization changes for user review.
For each file in the skill's references/ and scripts/ directories:
Classify each file with ${CLAUDE_SKILL_DIR}/references/license-compatibility-matrix.md (written
for an MIT target; it also lists common checklist and package licenses). Bundle compatible content
with the attribution header or license notice it requires; convert non-compatible content to the
matrix's URL Reference Pattern; mark GPL/LGPL tools as optional external dependencies; treat an
unknown license as incompatible (remove, or get permission).
Present license audit table:
| File | Source | License | Compatible? | Action |
|------|--------|---------|------------|--------|name and description per the Agent Skills spec, plus any field the target package's own validator requires)${CLAUDE_SKILL_DIR}/... path resolves to an actual filescripts/ have appropriate shebangsRun audit_skill.sh --strict one final time on the cleaned skill. Must return exit code 0.
Check whether the skill can run in common desktop-agent environments:
| Platform | Check |
|---|---|
| Claude Code | No hardcoded dependency on private ~/.claude paths unless documented. |
| Codex | SKILL.md is self-contained and installable under ~/.agents/skills/. |
| Cursor | A short .cursor/rules/*.mdc adapter can point to the canonical SKILL.md. |
| Windows | Commands avoid Unix-only assumptions or provide PowerShell/Python alternatives. |
| macOS/Linux | Shell examples use portable paths where possible. |
If the package is intended for a workshop or classroom, read
${CLAUDE_SKILL_DIR}/references/classroom-distribution.md and follow it (direct-download ZIPs,
release assets, classroom checklist).
Generate a table row matching the target package's README format:
| **{skill-name}** | {One-sentence description of what the skill does.} |Instruct the user to:
cp -r <cleaned_skill> ~/.claude/skills/<skill-name>/<skill-name> or relevant trigger phrasesGate: User confirms testing is complete.
cp -r <cleaned_skill_path> <target_package>/skills/<skill-name>/Apply the README entry drafted in Phase 5:
Present the exact commands but do NOT auto-execute push:
cd <target_package>
git add skills/<skill-name>/
git add README.md
git diff --cached # User reviews
git commit -m "Add <skill-name>: <one-line description>"Gate: User reviews git diff --cached and explicitly approves the commit. Push is always manual.
Remind the user to:
git clone <repo> && cp -r <repo>/skills/<skill-name> ~/.claude/skills/references/classroom-distribution.md.© Aperivue, 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 6 other files (scripts, references) in skills/publish-skill of Aperivue/medsci-skills.
Open the folder on GitHubat commit 3b14ae2
Publish Skill 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 |
|---|---|---|---|---|---|---|
| Publish Skill this skillAperivue/medsci-skills | 331 | — | ~3.2k | Automated safety check: Pass | MIT | |
| Hypothesis Generationspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 84k | 4 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 47k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Peer Reviewspacering-net/codeg | 3.9k | 17 repos | ~5.9k | Automated safety check: Notes | MIT |
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
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.
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
spacering-net/codeg
Structured manuscript/grant review with checklist-based evaluation.
mvanhorn/last30days-skill
Research what people actually say about any topic in the last 30 days.
Aperivue/medsci-skills
A skill your agent uses when turning a folder of research PDFs into Obsidian notes, even if Obsidian is not named.
Aperivue/medsci-skills
A skill your agent uses when a clinical CSV/Excel dataset needs profiling and cleaning before analysis (missing values, outliers, duplicates, type mismatches).
Aperivue/medsci-skills
A skill your agent uses when checking a radiology or medical AI study design before drafting or submission.
Aperivue/medsci-skills
A skill your agent uses when each author needs an ICMJE Conflict of Interest disclosure form (coidisclosure.docx) for submission.
Aperivue/medsci-skills
A skill your agent uses when an institutional Word form (.doc/.docx IRB protocol, ethics application, grant template) must be filled without breaking its styles, tables, fonts or page layout.
Aperivue/medsci-skills
A skill your agent uses when looking for research topics a longitudinal cohort database can answer (NHIS, UK Biobank, an institutional EMR or registry).
Categories
A skill your agent uses when turning a personal agent skill into an open-source, distributable one. Publish Skill is an agent skill from Aperivue/medsci-skills. Use when turning a personal agent skill into an open-source, distributable one.
Publish Skill fits situations like: turning a personal agent skill into an open-source; distributable one.
Run `npx skills add Aperivue/medsci-skills --skill publish-skill -a claude-code`. Or copy the skill folder (skills/publish-skill in Aperivue/medsci-skills) into .claude/skills/publish-skill in your project. Claude Code loads it when a task matches its description.
Run `npx skills add Aperivue/medsci-skills --skill publish-skill -a codex`. Or copy the skill folder (skills/publish-skill in Aperivue/medsci-skills) into .agents/skills/publish-skill 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 Aperivue/medsci-skills --skill publish-skill -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/publish-skill, .gemini/skills/publish-skill, .github/skills/publish-skill and .opencode/skills/publish-skill in your project.
Going by SKILL.md and its folder, Publish Skill needs a shell for the scripts in its folder and the command-line tools its instructions call (git and bash). Our summary lists: Python 3; A Bash shell.
SKILL.md contains no URLs. Its commands use git, which can reach the network depending on how they are called. 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
Publish Skill is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 3.2k tokens (SKILL.md is roughly 13k 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 2.3k tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Publish Skill: Hypothesis Generation (spacering-net/codeg, 3.9k stars), GitHub Deep Research (bytedance/deer-flow, 84k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars) and Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Aperivue (a GitHub organization) maintains it in Aperivue/medsci-skills, which has 331 GitHub stars. The repository holds 54 skills in this directory. The repository was last updated on October 5, 2026.
Source: Aperivue/medsci-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.