co-researcher

Co-Researcher: Academic Research Plugin for Claude Code

Co-Researcher is an academic research plugin for Claude Code, Gemini CLI, OpenAI Codex and OpenCode. It runs literature reviews, systematic reviews, peer review and citation checks inside the AI assistant you already use.

Searches run against real scholarly databases (OpenAlex, arXiv, Europe PMC), and every bibliography passes a verification gate that catches fabricated, mismatched, and retracted citations before output.

Installation

Platform	Install
Claude Code	/plugin marketplace add poemswe/co-researcher then /plugin install co-researcher
Gemini CLI	gemini extension install https://github.com/poemswe/co-researcher
Codex	Tell Codex: Fetch and follow instructions from https://raw.githubusercontent.com/poemswe/co-researcher/main/.codex/INSTALL.md
OpenCode	Tell OpenCode: Fetch and follow instructions from https://raw.githubusercontent.com/poemswe/co-researcher/main/.opencode/INSTALL.md
Other agents (skills.sh)	npx skills add poemswe/co-researcher (skills only, without the commands or the session-start hook)

Manual setup for each platform is in .codex/INSTALL.md and .opencode/INSTALL.md. From a local clone, Gemini users can run gemini extension link ., and Claude CLI users claude plugin marketplace add poemswe/co-researcher && claude plugin install co-researcher.

Commands

Task	Claude / Gemini	Codex
Research project	/research	$research
Critical analysis	/analyze	$analyze
Peer review	/review	$review

Everything else runs when you describe the task in plain language, and the matching skill starts on its own.

/research "remote work and productivity" drafts a plan and waits for your approval before running it. Add --auto to skip the approval, --plan-only to stop at the plan, or --template=quick|rigorous|comprehensive for a preset depth.

Skills

Each skill follows the Systemic Honesty principles, which a session-start hook loads automatically.

• literature-review: database search, screening and synthesis, with an evidence check before delivery
• systematic-review: PRISMA-standard systematic reviews
• research-synthesis: narrative synthesis with stated uncertainty
• multi-source-investigation: cross-checking claims across sources
• critical-analysis: logic checking and fallacy detection
• peer-review: manuscript critique and methodological review
• research-methodology: design selection and validation, including cross-domain and first-principles reframing
• hypothesis-testing: hypotheses, variables, falsification criteria, manipulation checks and scorer checks
• quantitative-analysis: test selection, power and effect sizes
• qualitative-research: coding and thematic analysis
• ethics-review: IRB compliance and privacy risk
• grant-writing: proposals and specific aims
• academic-writing: removing AI-isms from research prose
• research-manager: task planning and resumable project state
• using-co-researcher: orientation to the suite

Literature Reviews With Evidence Checks

Ask your agent for a literature review ("review the evidence on remote work and productivity"), or invoke the literature-review skill. The agent searches OpenAlex, arXiv and Europe PMC, screens what it finds, reads the full texts it can retrieve through legal open-access routes, and writes everything into a workspace under your current directory.

File in review/{slug}/	Holds
protocol.md	the question, inclusion criteria and query log
corpus.json	every candidate paper and its screening decision
papers/{key}/fulltext.md	the retrieved text of each included paper
synthesis.md	the review itself
claims.json	one entry per cited sentence, with the verbatim quote behind it
refs.json	the bibliography, checked against OpenAlex, Europe PMC and Crossref

Before delivering, the agent runs validate_review.py, which checks the workspace without a model. Every quote must occur in its paper, and every citation must point to exactly one screened paper. Every number in a claim must appear in its quote, and every cited sentence in the synthesis must agree with a verified claim in its numbers, negation and direction. A number in an uncited sentence is flagged. When a check fails, the agent receives the findings and up to three rounds to repair them.

The review arrives as	Meaning
valid	every check passed
valid with warnings	the checks passed, with caveats listed beside the review, such as support from an abstract only or a bibliography that could not be resolved online
INVALID EVIDENCE	problems remained after repair; the draft opens with this warning and names what failed, so treat it as unverified and ask the agent to fix those items or check them yourself

The checks confirm that the review says what its sources say. They do not confirm that the sources are right, and they cannot judge meaning, so a sentence that calls a finding "proven" where the paper says "suggested" passes. Read the review as critically as you would any draft.

To re-check a workspace yourself, run python3 /path/to/co-researcher/skills/literature-review/scripts/validate_review.py --workspace review/{slug}. Options, output formats and exit codes are in docs/validate-review.md.

How the checker was tested, what it catches and what still gets through are in the report, with a technical write-up behind it.

Research Toolchain

The scripts in skills/literature-review/scripts/ run through uv, and the other evidence-handling skills share them. Run bash scripts/setup.sh once to install uv and, optionally, store an OpenAlex API key.

Script	What it does
openalex_cli.py	cross-disciplinary search over about 250M works
search_arxiv.py	preprint search
europepmc_api.py	life-science full text and citation chaining
read_paper.py	DOI, arXiv ID or PMCID to markdown full text through legal open-access routes; warns on retractions
build_corpus.py	merges search results into a deduplicated corpus.json, keeping screening decisions on re-runs
verify_citations.py	resolves every citation against OpenAlex, Europe PMC and Crossref, and flags mismatched, not_found or retracted
prisma_counts.py	PRISMA 2020 flow counts from corpus.json
check_claims.py	checks each quote against its paper and each citation against the corpus
validate_review.py	the offline gate that runs every check and writes an auditable JSON report

Evaluations

The repository carries 34 broad quality cases across 10 capabilities, and a separate 16-case evidence-integrity set. Results are on the Evals dashboard. A broad quality score is not an integrity result. Running and publishing evals is covered in evals/README.md.

Development

PYTHONNOUSERSITE=1 uv run --no-project --with pytest --with 'pymupdf4llm<2' --with python-dotenv --with 'bibtexparser>=1.4,<2' python -m pytest -q tests

The suite runs offline on fixture data. tests/test_research_smoke.py alone covers claim checking, PRISMA counts and the resumable research scaffold. An opt-in Codex smoke needs an authenticated Codex CLI: CO_RESEARCHER_CODEX_SMOKE=1 uv run scripts/codex_smoke_research.py.

Path	Holds
skills/	the research skills, one source for every platform
commands/	platform commands (.md for Claude, .toml for Gemini)
.codex/, .opencode/	launchers and install instructions
evals/	quality and integrity cases, the runner and the dashboard
.claude-plugin/, gemini-extension.json, GEMINI.md	manifests

Star History

License

MIT. One optional runtime dependency, pymupdf4llm (with its PyMuPDF backend), is AGPL-3.0. read_paper.py uses it for PDF text extraction, and uv pulls it in only when that script runs. If you redistribute a service built on read_paper.py, the AGPL terms apply to that dependency. The Europe PMC JATS and OpenAlex abstract routes don't need it.