Use gene structure mapper for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

Lightweight Whole Slide Image (WSI) tiling and preprocessing for digital pathology; use when you need fast tissue detection and tile extraction to prepare datasets or run quick tile-based analysis.

Use idc-index to query and download public cancer imaging data from NCI Imaging Data Commons. Used to access large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Supports metadata querying, in-browser visualization, and license checking.

Comprehensive biosignal processing for ECG/PPG/EEG/EDA/RSP/EMG/EOG; use when you need to clean, segment, and extract physiological features for HRV, event-related responses, complexity metrics, or multimodal psychophysiology pipelines.

End-to-end Neuropixels extracellular electrophysiology analysis (SpikeGLX/Open Ephys/NWB) including preprocessing, motion correction, Kilosort4 spike sorting, QC metrics, and Allen/IBL-style curation; use when processing Neuropixels recordings or when users mention Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, drift/motion correction, or unit curation.

Statistical visualization library integrated with pandas; use it when you need fast EDA of distributions, relationships, and categorical comparisons (e.g., box/violin/pair plots and heatmaps) with strong default aesthetics on top of matplotlib.

Search and retrieve scientific preprints from arXiv; use it when you need to find papers by keyword/author/category, fetch metadata (abstract, DOI, PDF URL), or download PDFs for offline reading.

Use Bio.Entrez to access NCBI databases (e.g., PubMed/GenBank) for searching, fetching summaries, and downloading records when your workflow needs to call the NCBI E-utilities API over the network.

Comprehensive analytics tool for forecasting breakthrough therapeutic technologies by integrating multi-dimensional data sources including clinical development pipelines, intellectual property landscapes, and capital mar.

Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources.

Programmatic access to DrugBank drug and target data; use when you need to download, parse, and analyze DrugBank XML for properties, interactions, pathways, and pharmacology.

Access the European Nucleotide Archive (ENA) via REST APIs and FTP/Aspera to search and retrieve sequences, raw reads (FASTQ), assemblies, and metadata when you have accession IDs or need metadata-driven discovery for genomics pipelines.

Use grant gantt chart gen for evidence insight workflows that need structured execution, explicit assumptions, and clear output boundaries.

Access the Human Metabolome Database (HMDB) to search metabolites by name/structure/ID and extract chemical/biological/clinical fields when you need metabolomics research data or automated HMDB XML mining.

Produce a structured close-reading report from a paper's full PDF-to-Markdown text (with `## Page XX` pagination and image references) when you need to systematically extract background, research questions, methods, results, limitations, and reproducible experimental details.

Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D similarity) or automated structural data ingestion for structural biology and drug discovery workflows.

Automatically finds and ranks PubMed references for each sentence in scientific text; use when you need titles, DOIs, and brief recommendation reasons from the PubMed E-utilities API.

Download academic papers from open-access sources when the user provides a DOI/arXiv ID or requests a keyword-based paper search, and return the saved PDF path.

Access the ZINC (230M+ purchasable compounds) database when you need to look up compounds by ZINC ID/SMILES, run similarity/analog searches, or download 3D ready-to-dock structures for virtual screening and drug discovery.

Complete workflow for generating academic research posters from PDF literature; use when you need to extract paper content from PDFs and produce a LaTeX-based poster (beamerposter/tikzposter/baposter) with mandatory figure generation and a final rendered HTML deliverable.

Calculate Body Mass Index (BMI) and Body Surface Area (BSA) for clinical assessment, obesity screening, and chemotherapy dosing. Supports multiple BSA formulas (DuBois, Mosteller, Haycock), WHO weight classification, pediatric calculations, and metric/imperial input.

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Convert HTML files or URLs to high-fidelity PDFs using Puppeteer; auto-detects or forces RTL for Hebrew/Arabic when RTL content is present.

Import local literature into a managed library; trigger when you need offline deduplication, tagging, and a searchable index.

Interpret figures in academic papers and their captions when the input is a PDF-to-Markdown document with page markers and image links, producing a structured Markdown report for extracting variables, trends, and conclusions.

Convert files and Office documents into clean Markdown when you need LLM-friendly, token-efficient text (e.g., for summarization, search, RAG ingestion, or dataset preparation).

Interactive visualization library for Python. Use it when you need hover tooltips, zoom/pan, selection, animations, or charts embeddable in web pages (e.g., dashboards, exploratory analysis, presentations).

Automates publication-quality scientific diagrams (e.g., flowcharts, architectures, pathways) when you need journal/poster-ready visuals from a natural-language description.

Converts research text into a Mermaid technical roadmap flowchart. Use when the user provides research proposals, experiment designs, or scientific text and asks for a roadmap or flowchart.

Fix garbled text in PDF/SVG vector graphics caused by font encoding issues, making files editable in AI tools. Supports batch processing and JSON export for manual correction.

| What this skill does | What it does NOT do |

Panel data analysis with Python using linearmodels and pandas.

Run regression analyses in Stata with publication-ready output tables.

Clean and transform messy data in Stata with reproducible workflows

Build and verify replication packages — routes to reproducibility-auditor agent

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Explore methodological approaches through structured analysis before planning implementation

Document a recently solved research problem to compound methodological knowledge

Execute research implementation plans efficiently while maintaining estimation quality and finishing features

Extract TikZ diagrams from Beamer source, compile to PDF, convert to SVG with 0-based indexing. Use when updating TikZ diagrams for Quarto slides.

Run an end-to-end data analysis in R or Python: load, explore, analyze, and produce publication-ready output.

Submission pipeline — journal targeting, replication package, audit, and final gate. Replaces /submit, /target-journal, /audit-replication, /data-deposit.

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