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A 13-agent, PRISMA-capable research pipeline that runs scoping, systematic literature search, verification, synthesis, meta-analysis, and APA‑style reporting fo
AlterLab Deep Research is a comprehensive academic-research orchestration skill: it converts a research brief into a protocol, performs systematic literature searches, verifies sources, synthesizes evidence, assesses risk-of-bias, and compiles APA 7.0 or PRISMA-compliant reports. The skill includes a 13-agent team (research question formulation, bibliography, verification, synthesis, meta-analysis, editorial review, ethics, devil's advocate, monitoring, and more) to produce reproducible research outputs and monitoring configs.
Use when conducting rigorous academic work: systematic reviews, meta-analyses, literature reviews, policy analysis, or guided Socratic research where the user needs methodology design, curated bibliographies, evidence grading, or a full APA/PRISMA report. Also appropriate for quick briefs and fact-checking modes when a lighter pass is required.
Best paired with advanced multi-agent orchestrators and Claude/Gemma-style assistants that support tool chaining, long-form synthesis, and structured template rendering.
A comprehensive 13-agent academic research pipeline skill with 7 operational modes including PRISMA-compliant systematic review. No scripts to execute — purely instructional. Exceptionally well-documented with clear trigger conditions, failure paths, cross-agent quality alignment, and bilingual support (English/Chinese). The SKILL.md is thorough and production-quality, though the skill relies heavily on referenced sub-files (agents/, references/, templates/) that weren't available for review.
Impressive skill scope and documentation quality. Pure prompt-engineering skill with no executable scripts, which limits security concerns. The 2-point security deduction is for Bash being in allowed-tools without clear justification. Architecture is strong with good file organization and progressive disclosure. Usefulness is high for academic/research audience but niche outside that domain.
Mixed Methods Research Design
Comprehensive guide for designing and integrating qualitative and quantitative research approaches using established academic frameworks.
ClinVar Database (AlterLab)
Search and interpret NCBI ClinVar variant data, access via E-utilities or FTP, annotate VCFs, and incorporate review-status and evidence best practices for geno
AlterLab PyMC — Bayesian Modeling
Bayesian modeling workflow using PyMC (v5+): build hierarchical models, run MCMC (NUTS) or variational inference, diagnose sampling, and compare models with LOO
bioRxiv Database Search
Search and retrieve life-sciences preprints from bioRxiv via API.
Academic Statistical Analysis
Guided hypothesis testing, assumption checking, and APA-formatted reporting.
GeoPandas Geospatial Analysis
Advanced spatial analysis for vector data including coordinate reprojection, spatial joins, and choropleth mapping using the GeoPandas library.
DepMap Cancer Dependency Analysis
Query the Cancer Dependency Map (DepMap) for gene dependency scores, drug sensitivity, and cancer-specific genetic vulnerabilities.
Scite Database (Smart Citations)
Query Scite.ai Smart Citations by DOI to report supporting, contrasting, and mentioning citation counts and help assess a paper's reliability.
Research Information Lookup
Find and synthesize current research and academic papers with automatic backend routing (Parallel Chat API or Perplexity) and structured citations.
arXiv Paper Search & Download
Search arXiv, fetch paper metadata, download PDFs, and produce concise summaries for academic papers (ID or query).
Deep Research
Run multi-step autonomous research workflows: search, crawl, validate sources, and produce structured research reports and market analyses.
Ultimate Assistant — Comprehensive Response
Produces methodical, highly detailed step-by-step answers that integrate scientific and non-scientific perspectives for complex questions.
Scite Database
Fetch and summarize Scite.ai Smart Citations for a DOI to classify supporting, contrasting, and mentioning citations and assess a paper's reception.
Mixed Methods Research Design
Comprehensive guide for designing and integrating qualitative and quantitative research approaches using established academic frameworks.
ICLR Submission Workflow
Project management for ICLR submissions, from topic selection and anonymization to OpenReview discussion and final camera-ready.