Research

Survey existing compliance artifacts — policies, audits, certifications. Use when asked "what compliance docs do we have", "survey our policies", or "inventory our compliance artifacts".

Survey legal artifacts for audit readiness. Use when asked "are we audit ready", "what legal artifacts exist", or "survey our legal docs".

Inspect a remote host that is running the read-only `rpeek serve` diagnostic server. Use when the user wants to read logs, configs, process state, disk usage, or journald on a remote machine reachable via the `rpeek` client — e.g. "check why nginx is down on 10.0.0.5", "tail the app log on the prod box", "what's eating disk there". Do NOT use for the local machine (use normal shell tools) or for anything that writes/mutates — this server is read-only by design.

Use when the user needs research that settles a decision - market validation, build-or-buy, competitor and pricing scans, "is there demand for X", "where should we publish this", "what does the incumbent actually do". Produces a cited findings memo or report where every claim states how well it is supported. Triggers on "legwork", "deep research", "research report", "compare X vs Y", "should we build", "is there demand". Not for simple lookups, debugging, or anything one or two searches would...

Use when researching a question that requires multiple sources. Covers question decomposition, source evaluation, tracking what is known versus assumed, and producing a synthesis with honest confidence levels.

This skill should be used for advanced LLM evaluation: LLM-as-judge systems, direct scoring, pairwise comparison, rubric calibration, evaluator bias mitigation, confidence scoring, and automated quality assessment.

Ensure thorough validation, error recovery, and transparent reasoning in research tasks with multiple tool calls

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.

Produce auditable, evidence-first research and reports for public-interest, market, policy, product, academic, and fact-checking questions. Use this skill whenever a user asks to investigate a topic, compare options, verify claims, synthesize multiple sources, or write a research report that should be traceable claim by claim. Prioritize primary and authoritative sources, verify links and source relevance, separate facts from inferences, and state uncertainty explicitly. Do not use for simple...

Produce auditable, evidence-first research and reports for public-interest, market, policy, product, academic, and fact-checking questions. Use this skill whenever a user asks to investigate a topic, compare options, verify claims, synthesize multiple sources, or write a research report that should be traceable claim by claim. Prioritize primary and authoritative sources, verify links and source relevance, separate facts from inferences, and state uncertainty explicitly. Do not use for simple...

将模糊需求收敛为可执行的 DDD 建模输入：问题陈述、目标/非目标、约束、术语种子与风险清单。

协作式领域发现：通过事件风暴或领域故事讲述，产出事件流、命令/事件候选、热点与歧义清单。

Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confidence scores, performs functional enrichment analysis (GO/KEGG/Reactome), and optionally includes structural data. No API key required for core functionality (STRING). Use when analyzing protein networks, discovering interaction partners, identifying functional modules, or studying protein complexes.

Create compelling story-format summaries using UltraThink to find the best narrative framing. Support multiple formats - 3-part narrative, n-length with inline links, abridged 5-line, or comprehensive via Foundry MCP. USE WHEN user says 'create story explanation', 'narrative summary', 'explain as a story', or wants content in Daniel's conversational first-person voice.

Search PubMed biomedical literature with natural language queries powered by Valyu semantic search. Full-text access, integrate into your AI projects.

Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research. Access ChEMBL, PubMed, ClinicalTrials.gov, OpenTargets, OpenFDA, OMIM, Reactome, KEGG, UniProt, and more through a unified MCP endpoint. Use when researching disease targets, finding approved/investigational drugs, searching clinical evidence, discovering genetic associations, or analyzing compound bioactivity data.

Choose optimal external AI models for code analysis, bug investigation, and architectural decisions. Use when consulting multiple LLMs via claudish, comparing model perspectives, or investigating complex Go/LSP/transpiler issues. Provides empirically validated model rankings (91/100 for MiniMax M2, 83/100 for Grok Code Fast) and proven consultation strategies based on real-world testing.

Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu.

Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust. Drops detection-p-failed and low-bead-count probes, removes cross-reactive/non-specific probes (Chen 2013 / Pidsley 2016 lists via maxprobes), excludes SNP-overlapping probes with dropLociWithSnps, and handles sex-chromosome probes. Collapses EPICv2 replicate probes with betasCollapseToPfx and harmonizes across array versions (EPICv2 hg38 vs ...

Call germline SNPs and indels with GATK HaplotypeCaller and the GVCF joint-genotyping workflow. Covers the local-reassembly + PairHMM mechanism (why HC beats pileup callers on indels), the -ERC GVCF reference-confidence model and <NON_REF> allele, BQSR-vs-DRAGSTR and --dragen-mode error modeling, allele-specific (AS_) annotations, and edge cases (ploidy, Mutect2 mitochondria mode, sex chromosomes/PAR, contamination gating). Use when deciding whether to use HaplotypeCaller vs a pileup or DRAGE...

Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use wh...