Open Science Skills

A library of Claude Code skills for experimental social science, computational text analysis, manuscript QA, and transparent reporting. Install as a plugin to get AI assistance from research design through citation, figure/table, and final submission checks. All 23 skills auto-trigger from prompt context and are also available as explicit /oss:skill-name slash commands (the oss: prefix can be omitted when there is no ambiguity with other installed plugins).

Skills were developed using a curated library of methodology texts. They are iteratively expanded as new sources, ideas, and skills are incorporated. This is a living and breathing kind of repo. Skill building and editing is author-driven with the help of Opus 4.6, Gemini 3.0, and Chat GPT 5.4.

Design follows Anthropic's skill authoring best practices: concise procedural guidance (no textbook definitions), trigger-rich YAML descriptions for auto-invocation, and progressive disclosure (instructions in skills, bibliography in SOURCES.md). Skills are periodically audited against both the Claude Code skills reference and the skill authoring guide to keep descriptions, frontmatter, and substantive content current.

These skills are meant to support, not supplant, the research and writing process. They adhere to APSA, JARS, DA-RT, TOP, and FAIR open-science expectations. All guidance is grounded in 160+ published sources and documented workflow patterns — see SOURCES.md for the full bibliography.

Skill Map

flowchart LR
    A[Research Design] --> B[Analysis]
    A --> C[Writing and PAP]
    B --> D[Methods Reporting]
    C --> D
    D --> E[Manuscript QA and FAIR]
    E --> F[Review and Submission]

    A -.-> A1[conjoint / survey / list / cross-national]
    B -.-> B1[topic modeling / text classification / OCR]
    C -.-> C1[hypotheses / literature review / narrative / preregistration]
    D -.-> D1[figures / tables / methods reporting]
    E -.-> E1[FAIR / citations / figure-table-audit / archive checks]
    F -.-> F1[paper-review-lite / presubmit / journal-review]

Use the domain skills when designing or analyzing a study. Use the manuscript-QA skills when a draft exists and you need to check whether FAIR availability, citations, figures, tables, reporting, and replication materials can survive review.

How Skills Work

Each skill is available in two ways:

Mode	How	When to use
Auto-trigger	Claude reads your prompt and loads the relevant skill silently	Working naturally — Claude detects context
Slash command	Type `/oss:skill-name` (or just `/skill-name` when there is no ambiguity)	When you want to invoke a skill explicitly

Both modes are available when installed as a plugin. Individual skills can also be installed manually (auto-trigger only).

Installation

Option 1 — Plugin (recommended, installs all skills + slash commands)

Permanent install (user-wide, persists across all projects):

# Step 1: Register the marketplace (one-time)
claude plugin marketplace add scdenney/open-science-skills

# Step 2: Install the plugin
claude plugin install oss@open-science-skills

# Project-only install
claude plugin install oss@open-science-skills --scope project

The plugin's slash-command prefix is oss: (short for open science skills). The marketplace and GitHub repo are still named open-science-skills.

Session-only (no install required, active for the current session):

git clone https://github.com/scdenney/open-science-skills.git
cd open-science-skills && claude --plugin-dir ./plugin

All 23 skills auto-trigger based on your prompts. All 23 slash commands (/oss:conjoint-design, /oss:fair-check, /oss:figures, /oss:tables, /oss:figure-table-audit, etc.) are immediately available. The prefix can be omitted when there is no ambiguity with other installed plugins.

Option 2 — Selective install (choose specific skills, auto-trigger only)

Use the interactive install script to pick only the skills you want:

git clone https://github.com/scdenney/open-science-skills.git
cd open-science-skills
bash plugin/scripts/install.sh

The script lists available skills and lets you choose interactively. Skills are installed to ./.claude/skills/ by default (current project only). Options:

# Install to user-wide skills directory (all projects)
bash plugin/scripts/install.sh --target ~/.claude/skills

# Install specific skills non-interactively
bash plugin/scripts/install.sh --skill conjoint-design survey-design list-experiment

# Install all skills
bash plugin/scripts/install.sh --all --target ~/.claude/skills

Restart Claude Code after installing to load the new skills.

Option 3 — Manual copy (single skill, auto-trigger only)

git clone https://github.com/scdenney/open-science-skills.git

# Project-level (current project only)
mkdir -p your-project/.claude/skills/conjoint-design
cp open-science-skills/plugin/skills/conjoint-design/SKILL.md \
   your-project/.claude/skills/conjoint-design/SKILL.md

# User-wide (all projects)
mkdir -p ~/.claude/skills/list-experiment
cp open-science-skills/plugin/skills/list-experiment/SKILL.md \
   ~/.claude/skills/list-experiment/SKILL.md

Note: Manual install gives you auto-trigger only. Slash commands (/skill-name) require the plugin.

Skills

Research Design

Skill	Slash command	What it does
conjoint-design	`/conjoint-design`	Attribute architecture, AMCE/AMIE estimation, power analysis (`cjpowR`), BART heterogeneity detection, design variants
conjoint-diagnostics	`/conjoint-diagnostics`	Diagnostic checklist: design, estimation, measurement error (IRR), external validity, interpretation
conjoint-cleaning	`/conjoint-cleaning`	Qualtrics export to analysis-ready format: column conventions, reshaping, choice mapping, translation, pilot detection, validation
survey-design	`/survey-design`	Question construction, scale design, survey flow, pretesting, respondent burden, social desirability mitigation
cross-national-design	`/cross-national-design`	Cross-national survey experiments: per-country power, sensitivity bias auditing, instrument localization
list-experiment	`/list-experiment`	Item count technique: pre-design sensitivity assessment, control list design, NLSreg/MLreg estimation, assumption testing, placebo diagnostics

Analysis

Skill	Slash command	What it does
topic-modeling	`/topic-modeling`	STM with metadata covariates, topic count selection via coherence-exclusivity diagnostics, reporting
text-classification	`/text-classification`	LLM-based classification: codebook design, learning regime selection, human-LLM hybrid workflows, validation

Corpus Processing

Skill	Slash command	What it does
vlm-ocr-pipeline	`/vlm-ocr-pipeline`	VLM-based OCR: model selection, image handling, prompt engineering, batch strategy, accuracy evaluation, reproducibility
post-ocr-cleanup	`/post-ocr-cleanup`	Post-OCR cleanup: LLM and rule-based correction, quality diagnostics, multilingual considerations, corpus-level QA, provenance

Writing & Reporting

Skill	Slash command	What it does
hypothesis-building	`/hypothesis-building`	Falsifiability, counterfactuals, DAGs, FPCI, three-level hypothesis specification, equivalence testing, SESOI
literature-review	`/literature-review`	Evidence maps, closest-prior-work assessment, gap verdicts, literature clusters, synthesis plans
narrative-building	`/narrative-building`	Introduction logic, literature reviews, the "Why-to-If-Then" funnel, cumulative framing, multi-experiment coherence
pre-registration-writing	`/pre-registration-writing`	PAP structure, registry selection, analytical strategy specification, code pre-registration, deviation documentation
methods-reporting	`/methods-reporting`	40-item reporting checklist: CONSORT standards, JARS preregistration elements, DA-RT transparency

Figures & Tables

Skill	Slash command	What it does
figures	`/figures`	Design publication-quality figures: chart choice from comparison, scales, color, legend ordering matched to visual order, self-contained captions, reproducibility
tables	`/tables`	Design publication-quality tables: column order matching the argument, row grouping, precision and uncertainty conventions, self-contained titles and notes, code-generated workflows

Manuscript QA

Skill	Slash command	What it does
fair-check	`/fair-check`	FAIR audit for completed manuscripts: data/code/material availability, repository metadata, persistent identifiers, licenses, access restrictions, reuse conditions
citation-check	`/citation-check`	In-text/reference parity, DOI and source-status checks, stale working papers, citation-style and support audits
figure-table-audit	`/figure-table-audit`	End-stage QA of the finished figure/table set: inventory, cross-references, text-to-table consistency, accessibility, SI and replication linkage. Pairs with `figures` and `tables` (production-stage).

Review & Submission

Skill	Slash command	What it does
paper-review-lite	`/paper-review-lite`	Critical-Reviewer-style pre-submission audit: parallel quote-grounded sub-agents, verification cross-check, CONSORT + pre-reg audit for experimental papers. Lite counterpart to the standalone `presubmit` CLI.
presubmit	`/presubmit`	Activator + setup wizard for the standalone `presubmit` Python CLI: walks first-time users through install (venv + `pip install -e .`), Anthropic API key setup, and output location, then runs the heavier 30+ stage adversarial pipeline (resumable, cost-tracked, optional `--math` and `--code-dir` add-ons). Heavier API-driven counterpart to `paper-review-lite`.
journal-review	`/journal-review`	Drafts a senior-peer referee report on someone else's manuscript for a social-science journal. Five parallel finder sub-agents (Breaker, Butcher, Shredder, Void, Situator) + Blue Team filter + Chief Reviewer synthesis + Tone Guard sanitization produce a tight 1,200–2,000 word report (Recommendation + Summary + Major Concerns + Additional Concerns + Suggestions for Revision). Different role from `paper-review-lite` and `presubmit`, which are calibrated for SELF-AUDIT; this one is third-party referee work appropriate to send to a journal editor.

Contributing

PRs welcome. To add a new skill:

Create plugin/skills/<name>/SKILL.md following the skill authoring best practices
Add plugin/commands/<name>.md (see existing examples — one paragraph activation prompt + $ARGUMENTS)
Add sources to SOURCES.md under a new or existing section
Update badges and table in this README
Run bash plugin/scripts/check.sh before opening a PR

License

This project is licensed under Creative Commons Attribution-NonCommercial 4.0 International. The skills are intended for noncommercial scholarly and educational use.

The citation-check, literature-review, figures, tables, and figure-table-audit skills remix workflow ideas from Cheng-I Wu's Academic Research Skills for Claude Code, also licensed CC BY-NC 4.0. The instructions here are rewritten for this repository's open-science and experimental-social-science scope.