Claude Code: Research & Analysis Workflows

Use when a complete research workflow — its instructions, skills, data boundaries, and tool connections — must be assessed for portability across AI agents or environments, so each component is explicitly mapped before migration rather than assumed to transfer.

Use when a Claude Code session loops, drifts from scope, claims a fix that CI rejects, hits context, PATH, or permission walls, or fails in a way another retry will not solve and a root cause diagnosis is needed instead.

Use when AI contribution metadata must match the actual workflow, when model alias and dated identifiers need auditing, when verified and fabricated citation counts feed a release decision, or when a venue's AI disclosure statement needs evidence behind it.

Use when a draft in Turkish, English, or both reads as AI-generated and needs revision that removes machine writing patterns and translation calques while preserving meaning, citations, statistics, and the author's voice.

Use when a reference list needs APA 7 cleanup, when DOIs must be confirmed real against Crossref or PubMed, when the user asks whether AI-suggested citations actually exist, or when a manuscript needs a citation hygiene pass before submission or defense.

Use when authorship order, CRediT contribution roles, or AI-assistance attribution must be recorded transparently for a manuscript, when an author dispute needs an evidence trail, or before a contributorship statement is required at submission; this skill maintains the human-attribution ledger of who contributed what and in which role (authorship order, CRediT taxonomy, revision responsibilities), which is distinct from the disclosure-metadata audit owned by ai-disclosure-auditor.

Use when paired tr.md and en.md files need a parity verdict, when titles, frontmatter, headings, or DOI sets may have drifted between languages, or when a bilingual document is approaching release and its translation coverage needs an audit.

Use when drafting a manuscript, thesis chapter, or abstract that must exist in Turkish and English, when the user asks how to keep two language versions aligned, or when an IMRAD skeleton with word budgets is needed before writing starts.

Use when building slides, a poster, or a lightning talk from a manuscript, when a presentation must exist in Turkish and English, or when conference visuals need a traceability check so every number on a slide matches the analysis behind it.

Use when an ethics committee or IRB application involves AI anywhere in the pipeline, when KVKK, GDPR, or EU AI Act duties must be mapped to a study, or when consent and disclosure language about AI use needs drafting before submission.

Use when choosing a journal for a finished or nearly finished manuscript, when index status in Scopus, SSCI, ESCI, or TR Dizin must be confirmed, when a venue looks predatory, or when a cover letter needs drafting from the manuscript's actual claims.

Use when choosing or configuring MCP servers for research work, when a literature, reference manager, or scholarly search server needs a trust check before installation, or when an existing research tool stack needs a data flow and permission audit.

Use when a research note system needs architecture, when MOCs, frontmatter standards, and retrieval patterns must be designed for years of work, or when an existing vault has outgrown its structure and must migrate without breaking years of links.

Use when serving as a peer reviewer and deciding whether and how AI may assist, when a manuscript under review must never be pasted into an external tool, or when a confidentiality-preserving review and disclosure are needed.

Use when a systematic, scoping, or rapid review needs a reproducible pipeline: protocol framing (PICO/SPIDER/PCC), a logged search string, title/abstract and full-text screening with recorded exclusion reasons, and PRISMA flow counts, with the human as the deciding screener.

Use when adapting academic findings for a public audience (op-ed, social post, podcast) and the simplification must stay evidence-faithful, avoid overclaiming, respect embargoes, and disclose AI assistance.

Use when coding interviews, focus groups, or open-ended responses with AI assistance, when a codebook needs building or auditing, when intercoder reliability must be computed, or when qualitative quotes need integrity checks before publication.

Use when reviewer comments arrive and each one needs a tracked decision, when a revise and resubmit letter must map every comment to a manuscript change, or when contradictory reviewer demands need evidence-based, editor-facing framing.

Use when a source must be reached through DergiPark, ULAKBIM TR Dizin, HEAL-Link, YOK Thesis Center, or an institutional library route, when off-campus access fails, or when a lawful retrieval plan is needed for Turkish, Greek, or European materials.

Use before a tag, GitHub release, or Zenodo archive, when README, CATALOG, CHANGELOG, CITATION.cff, the disclosure aggregate, and skill discovery must agree, or when a go or no-go release verdict needs recorded evidence behind it.

Use when a researcher asks where to start, which project skill fits the current stage of a study, or in what order literature scoping, source access, vault upkeep, drafting, citation verification, disclosure, and review response should run.

Use when automating research session rituals in Claude Code with hooks, such as session-start context injection, daily research logging, session-end persistence, or pre-commit guards that block secrets and unverified citations.

Use when starting a literature review and a defensible search plan is needed, when database lanes and language layers must be chosen, when DOI coverage policy is unclear, or when inclusion and exclusion criteria need drafting before any source is read.

Use when sources must stay traceable across sessions and years, when each reference needs a passport recording where it was found, how it was verified, and where it is cited, or when a draft needs a cited-but-unverified sweep before submission.