Peer Review
K-Dense-AI/claude-scientific-writer
Prepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments.
Pre-registration, open data, and FAIR principles for research
Install Open Science Guide
$ npx skills add wentorai/research-plugins --skill open-science-guide -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install wentorai/research-plugins open-science-guide --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/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/research/funding/open-science-guide .claude/skills/open-science-guide && 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 "open-science-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/funding/open-science-guide into .claude/skills/open-science-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "open-science-guide", 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/wentorai/research-plugins/tree/main/skills/research/funding/open-science-guideType 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 wentorai/research-plugins --skill open-science-guide -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install wentorai/research-plugins open-science-guide --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/research/funding/open-science-guide .agents/skills/open-science-guide && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "open-science-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/funding/open-science-guide into .agents/skills/open-science-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "open-science-guide", 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 wentorai/research-plugins --skill open-science-guide -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install wentorai/research-plugins open-science-guide --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/research/funding/open-science-guide .cursor/skills/open-science-guide && 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 "open-science-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/funding/open-science-guide into .cursor/skills/open-science-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "open-science-guide", 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/wentorai/research-plugins.git --path skills/research/funding/open-science-guide--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 wentorai/research-plugins --skill open-science-guide -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install wentorai/research-plugins open-science-guide --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/research/funding/open-science-guide .gemini/skills/open-science-guide && 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 "open-science-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/funding/open-science-guide into .gemini/skills/open-science-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "open-science-guide", 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 wentorai/research-plugins open-science-guideInstalls 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 wentorai/research-plugins --skill open-science-guide -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/research/funding/open-science-guide .github/skills/open-science-guide && 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 "open-science-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/funding/open-science-guide into .github/skills/open-science-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "open-science-guide", 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 wentorai/research-plugins --skill open-science-guide -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install wentorai/research-plugins open-science-guide --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/research/funding/open-science-guide .opencode/skills/open-science-guide && 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 "open-science-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/funding/open-science-guide into .opencode/skills/open-science-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "open-science-guide", 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
open-science-guide- GitHub stars
- 298
- Used in
- 1 other repo
- Token cost
- ~2.3k tokens
- SKILL.md length
- 459 words
- Files
- 1
- Skills in repo
- 405
- Repo updated
- First seen
- Licence
- MIT
At a glance
Pre-registration, open data, and FAIR principles for research
- Works in 6 steps: Anonymize: Remove direct identifiers… → Aggregate: Share summary statistics or… → Restricted access: Deposit data with… → …
- Tasks that involve Reproducible research
- SKILL.md covers Why Open Science?, Pre-Registration, Registered Reports and FAIR Data Principles, plus 3 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Open Science Guide is an agent skill from wentorai/research-plugins. Pre-registration, open data, and FAIR principles for research
Its SKILL.md is about 2.3k 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 Reproducible research. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.
When your agent uses it
- Tasks that involve Reproducible research
Example prompts
- “/open-science-guide”
Workflow steps
6 steps, taken from the first numbered list in SKILL.md.
- Anonymize: Remove direct identifiers (name, email, IP) and indirect identifiers (rare combinations of demographics)
- Aggregate: Share summary statistics or aggregated data instead of individual-level data
- Restricted access: Deposit data with access controls (e.g., ICPSR restricted-use data)
- Synthetic data: Generate synthetic datasets that preserve statistical properties
- Controlled access: Use data use agreements (DUAs) for sensitive data
- Code without data: At minimum, share analysis code so methods are transparent
What it can do on your machine
Read from SKILL.md and the folder at commit bf44b3c. 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
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.
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
Open Science Guide loads about 2.3k tokens when it runs. Until then it costs about 20 tokens; SKILL.md has 459 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
The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 459 words, ~2,274 tokens.
Download SKILL.mdSave it as
.claude/skills/open-science-guide/SKILL.md (or your agent's skills folder).- name
- open-science-guide
- description
- Pre-registration, open data, and FAIR principles for research
Open Science Guide
Implement open science practices including study pre-registration, open data sharing, registered reports, and FAIR data principles to increase research transparency and reproducibility.
Why Open Science?
Open science practices address the replication crisis and increase trust in research findings:
| Practice | Problem It Addresses |
|---|---|
| Pre-registration | Prevents HARKing (hypothesizing after results are known) and p-hacking |
| Open data | Enables verification, reanalysis, and meta-analyses |
| Open materials | Allows exact replication of studies |
| Open access | Removes paywalls that limit access to knowledge |
| Registered reports | Eliminates publication bias (acceptance before results are known) |
| Open code | Enables computational reproducibility |
Pre-Registration
What to Pre-Register
Pre-registration commits you to your research plan before seeing the data:
Pre-registration template (standard fields):
1. HYPOTHESES
- H1: [Specific, directional hypothesis]
- H2: [Another hypothesis]
2. DESIGN
- Study type: [Experiment / Survey / Observational]
- Between/within subjects design: [Details]
- Conditions: [List experimental conditions]
3. SAMPLING PLAN
- Sample size: [N = X, justified by power analysis]
- Stopping rule: [When will data collection stop?]
- Inclusion/exclusion criteria: [List]
4. VARIABLES
- Independent variables: [List with levels]
- Dependent variables: [List with measurement details]
- Covariates: [List any control variables]
5. ANALYSIS PLAN
- Primary analysis: [Exact statistical test, e.g., "2x3 mixed ANOVA"]
- Secondary analyses: [Additional planned analyses]
- Inference criteria: [alpha level, correction for multiple comparisons]
- Exclusion criteria: [How will outliers or failed attention checks be handled?]
- Missing data: [How will missing data be handled?]
6. OTHER
- Exploratory analyses: [Analyses not tied to specific hypotheses]Where to Pre-Register
| Platform | URL | Disciplines | Features |
|---|---|---|---|
| OSF Registries | osf.io/registries | All | Free, flexible templates, versioned |
| AsPredicted | aspredicted.org | Social sciences, psychology | Simple 9-question form, private until shared |
| ClinicalTrials.gov | clinicaltrials.gov | Clinical research | Required for clinical trials (FDA) |
| PROSPERO | crd.york.ac.uk/prospero | Systematic reviews | Health-related reviews only |
| AEA RCT Registry | socialscienceregistry.org | Economics | RCTs in social sciences |
Pre-Registration Workflow
1. Design your study
2. Write the pre-registration document
3. Have a colleague review it
4. Submit to a registration platform
5. Receive a time-stamped registration (URL + DOI)
6. Collect and analyze data following the pre-registered plan
7. Report results transparently:
- Confirmatory analyses (pre-registered)
- Exploratory analyses (clearly labeled as exploratory)
8. Link the pre-registration in your manuscriptRegistered Reports
Registered Reports are a publication format where peer review occurs before data collection:
Stage 1 (Before Data Collection):
- Submit introduction, methods, and analysis plan
- Peer review evaluates the research question and methodology
- If accepted: "In-Principle Acceptance" (IPA)
- Paper will be published regardless of results
Stage 2 (After Data Collection):
- Collect data following the approved protocol
- Analyze and report results
- Add discussion section
- Final peer review checks adherence to protocol
- PublicationOver 300 journals now accept Registered Reports. Check the registry at cos.io/rr.
Benefits of Registered Reports
- Eliminates publication bias (null results are published)
- Ensures methodological rigor is reviewed before sunk costs
- Prevents post-hoc changes to hypotheses or analyses
- Provides certainty of publication to researchers
FAIR Data Principles
FAIR principles ensure research data is Findable, Accessible, Interoperable, and Reusable:
Findable
- F1: Data are assigned a globally unique, persistent identifier (DOI)
- F2: Data are described with rich metadata
- F3: Metadata include the identifier of the data
- F4: Data are registered or indexed in a searchable resource
Actions:
- Deposit data in a repository that assigns DOIs
- Write a comprehensive README and data dictionary
- Use standard metadata schemas (Dublin Core, DataCite)Accessible
- A1: Data are retrievable by their identifier using open protocols (HTTP)
- A2: Metadata remain accessible even if data are no longer available
Actions:
- Use established repositories (not personal websites)
- Specify access conditions clearly (open, restricted, embargoed)
- Even if data cannot be shared, publish metadata describing themInteroperable
- I1: Data use a formal, accessible, shared language (e.g., CSV, JSON, RDF)
- I2: Data use vocabularies that follow FAIR principles
- I3: Data include qualified references to other data
Actions:
- Use standard file formats (CSV, not proprietary Excel)
- Use standard variable names and coding schemes
- Link to related datasets using DOIsReusable
- R1: Data are richly described with provenance information
- R2: Data are released with a clear, accessible data usage license
- R3: Data meet domain-relevant community standards
Actions:
- Include a data dictionary with variable descriptions
- Apply a license (CC-BY 4.0 recommended)
- Describe data collection procedures, cleaning steps, and known issues
- Include analysis code alongside dataData Sharing Platforms
| Repository | Disciplines | Max Size | DOI | Cost |
|---|---|---|---|---|
| Zenodo | All | 50 GB | Yes | Free |
| Dryad | All (focus on sciences) | Unlimited | Yes | Sliding scale |
| Figshare | All | 20 GB (free) | Yes | Free/institutional |
| OSF | All | 5 GB (free) | Yes | Free |
| Harvard Dataverse | All (focus on social science) | 2.5 GB per file | Yes | Free |
| ICPSR | Social science | Varies | Yes | Free deposit |
| GenBank | Genomics | N/A | Accession numbers | Free |
| Protein Data Bank | Structural biology | N/A | PDB IDs | Free |
Show full SKILL.md (148 more words)Show less
Data Sharing Best Practices
README Template for Data Deposits
# Dataset: [Title]
## Description
Brief description of the dataset and the study it comes from.
## Citation
If you use this data, please cite:
[Full citation of the associated publication]
## File Description
- `data_raw.csv` - Raw data as collected (N = 500, 45 variables)
- `data_processed.csv` - Cleaned data after exclusions (N = 467, 38 variables)
- `codebook.csv` - Variable descriptions, types, and valid ranges
- `analysis_script.R` - Complete analysis code reproducing all results
## Variables (data_processed.csv)
| Variable | Type | Description | Valid Range |
|----------|------|-------------|-------------|
| participant_id | string | Unique participant identifier | P001-P500 |
| age | integer | Age in years | 18-65 |
| condition | categorical | Experimental condition | control, treatment_a, treatment_b |
| score_pre | numeric | Pre-test score | 0-100 |
| score_post | numeric | Post-test score | 0-100 |
## Missing Data
- 33 participants excluded for failing attention checks
- 12 missing values in `score_post` (participants did not complete)
- Missing coded as NA
## License
CC-BY 4.0 International
## Contact
[Name, email, ORCID]Sensitive Data Considerations
When data cannot be fully shared (e.g., due to participant privacy):
- Anonymize: Remove direct identifiers (name, email, IP) and indirect identifiers (rare combinations of demographics)
- Aggregate: Share summary statistics or aggregated data instead of individual-level data
- Restricted access: Deposit data with access controls (e.g., ICPSR restricted-use data)
- Synthetic data: Generate synthetic datasets that preserve statistical properties
- Controlled access: Use data use agreements (DUAs) for sensitive data
- Code without data: At minimum, share analysis code so methods are transparent
Open Science Badges
Many journals award badges for open science practices:
| Badge | Meaning |
|---|---|
| Open Data | Data publicly available |
| Open Materials | Research materials publicly available |
| Preregistered | Study pre-registered before data collection |
| Preregistered + Analysis Plan | Preregistered with detailed analysis plan |
These badges (developed by COS) appear on published articles and signal commitment to transparency.
© wentorai, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/research/funding/open-science-guide of wentorai/research-plugins.
Open the folder on GitHubat commit bf44b3c
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Open Science Guide 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 |
|---|---|---|---|---|---|---|
| Open Science Guide this skillwentorai/research-plugins | 298 | 1 repos | ~2.3k | Automated safety check: Pass | MIT | |
| Peer ReviewK-Dense-AI/claude-scientific-writer | 2.4k | 2 repos | ~3.1k | Automated safety check: Notes | MIT | |
| CHARLS Paper Reproduction Guidexjtulyc/MedgeClaw | 617 | 1 repos | ~1.8k | Automated safety check: Pass | None | |
| Compute Environment Setupaipoch/open-science | 5.5k | — | ~2.6k | Automated safety check: Pass | Apache-2.0 | |
| Figure Styleaipoch/open-science | 5.5k | — | ~5.1k | Automated safety check: Pass | Apache-2.0 | |
| Add Bactopia Toolbactopia/bactopia | 522 | — | ~4.1k | Automated safety check: Pass | MIT |
Similar skills
CHARLS Paper Reproduction Guide
xjtulyc/MedgeClaw
Guides an agent through reproducing papers built on the CHARLS health and retirement survey, from variable mapping to cognition, depression and isolation scores.
Compute Environment Setup
aipoch/open-science
Prepares setup instructions and a named activation file for a user-managed software environment on an Open-Science SSH or Slurm compute host.
Figure Style
aipoch/open-science
Publication-grade correctness and legibility rules for final-deliverable scientific figures, not exploratory plots.
Add Bactopia Tool
bactopia/bactopia
Scaffold a complete Bactopia Tool across all three tiers -- module, subworkflow, and workflow entry point under workflows/bactopia-tools/.
Modeling Code and Result Contracts
yushui2022/MathModel-Skill
Generates result-evidence contracts, tables and runnable q1 to q3 modeling code scaffolds for a math modeling paper from a model route, a data plan and cleaned data.
More from wentorai/research-plugins
All 405 skills in this repoAbstract Writing Guide
wentorai/research-plugins
Craft structured research abstracts that maximize clarity and journal acceptance
Academic Citation Manager
wentorai/research-plugins
Manage academic citations across BibTeX, APA, MLA, and Chicago formats
Academic Paper Summarizer
wentorai/research-plugins
Summarize academic papers with structured extraction of key elements
Academic Study Methods
wentorai/research-plugins
Evidence-based study techniques for academic learning and retention
Academic Tone Guide
wentorai/research-plugins
Adjust writing tone and register for academic audiences and venues
Academic Translation Guide
wentorai/research-plugins
Academic translation, post-editing, and Chinglish correction guide
Related
Categories
Questions about Open Science Guide
What does Open Science Guide do?
Pre-registration, open data, and FAIR principles for research. Open Science Guide is an agent skill from wentorai/research-plugins.
When should I use Open Science Guide?
Open Science Guide fits situations like: tasks that involve Reproducible research.
How do I install Open Science Guide in Claude Code?
Run `npx skills add wentorai/research-plugins --skill open-science-guide -a claude-code`. Or copy the skill folder (skills/research/funding/open-science-guide in wentorai/research-plugins) into .claude/skills/open-science-guide in your project. Claude Code loads it when a task matches its description.
How do I install Open Science Guide in Codex?
Run `npx skills add wentorai/research-plugins --skill open-science-guide -a codex`. Or copy the skill folder (skills/research/funding/open-science-guide in wentorai/research-plugins) into .agents/skills/open-science-guide in your project. Codex loads it when a task matches its description.
Can I use Open Science Guide 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 wentorai/research-plugins --skill open-science-guide -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/open-science-guide, .gemini/skills/open-science-guide, .github/skills/open-science-guide and .opencode/skills/open-science-guide in your project.
What does Open Science Guide need to run?
SKILL.md names no scripts, command-line tools or credentials: Open Science Guide is instructions for the agent only.
Does Open Science Guide 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 Open Science Guide 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 Open Science Guide use?
Open Science Guide is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Open Science Guide use?
About 2.3k tokens (SKILL.md is roughly 9.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Open Science Guide?
Skills that share tags, products or a category with Open Science Guide: Peer Review (K-Dense-AI/claude-scientific-writer, 2.4k stars), CHARLS Paper Reproduction Guide (xjtulyc/MedgeClaw, 617 stars), Compute Environment Setup (aipoch/open-science, 5.5k stars) and Figure Style (aipoch/open-science, 5.5k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Open Science Guide?
wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.
Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.