Processing
Data transformation and parsing
clinical-decision-support-documents
by jaechang-hits
"Guidelines for generating clinical decision support (CDS) documents: patient cohort analyses (biomarker-stratified outcomes) and treatment recommendation reports (GRADE-graded evidence). Covers document structure, executive summary design, evidence grading (GRADE 1A–2C), statistical reporting (HR, CI, survival), and biomarker integration. Use when creating pharmaceutical research documents, clinical guidelines, or regulatory submissions."
flowio-flow-cytometry
by jaechang-hits
"Parse and create FCS (Flow Cytometry Standard) files v2.0-3.1. Read event data as NumPy arrays, extract channel metadata, handle multi-dataset files, export to CSV/FCS. For advanced gating and compensation use FlowKit."
tilt
by aiskillstore
Manages Tilt development environments via CLI and Tiltfile authoring. Must use when working with Tilt or Tiltfiles.
python-best-practices
by aiskillstore
Provides Python patterns for type-first development with dataclasses, discriminated unions, NewType, and Protocol. Must use when reading or writing Python files.
plugin-structure
by aiskillstore
This skill should be used when the user asks to "create a plugin", "scaffold a plugin", "understand plugin structure", "organize plugin components", "set up plugin.json", "use ${CLAUDE_PLUGIN_ROOT}", "add commands/agents/skills/hooks", "configure auto-discovery", or needs guidance on plugin directory layout, manifest configuration, component organization, file naming conventions, or Claude Code plugin architecture best practices.
docx
by aiskillstore
"Comprehensive document creation, editing, and analysis with support for tracked changes, comments, formatting preservation, and text extraction. When Claude needs to work with professional documents (.docx files) for: (1) Creating new documents, (2) Modifying or editing content, (3) Working with tracked changes, (4) Adding comments, or any other document tasks"
xlsx
by aiskillstore
"Comprehensive spreadsheet creation, editing, and analysis with support for formulas, formatting, data analysis, and visualization. When Claude needs to work with spreadsheets (.xlsx, .xlsm, .csv, .tsv, etc) for: (1) Creating new spreadsheets with formulas and formatting, (2) Reading or analyzing data, (3) Modify existing spreadsheets while preserving formulas, (4) Data analysis and visualization in spreadsheets, or (5) Recalculating formulas"
linear
by aiskillstore
Manages Linear issues, teams, and projects via CLI. Lists issues, creates tasks, views details, links issues, and runs GraphQL queries. Must use for "my Linear issues", "create Linear task", "link issues in Linear", "Linear API query", or any Linear project management request.
mcp-integration
by aiskillstore
This skill should be used when the user asks to "add MCP server", "integrate MCP", "configure MCP in plugin", "use .mcp.json", "set up Model Context Protocol", "connect external service", mentions "${CLAUDE_PLUGIN_ROOT} with MCP", or discusses MCP server types (SSE, stdio, HTTP, WebSocket). Provides comprehensive guidance for integrating Model Context Protocol servers into Claude Code plugins for external tool and service integration.
mcp-builder
by aiskillstore
Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).
hook-development
by aiskillstore
This skill should be used when the user asks to "create a hook", "add a PreToolUse/PostToolUse/Stop hook", "validate tool use", "implement prompt-based hooks", "use ${CLAUDE_PLUGIN_ROOT}", "set up event-driven automation", "block dangerous commands", or mentions hook events (PreToolUse, PostToolUse, Stop, SubagentStop, SessionStart, SessionEnd, UserPromptSubmit, PreCompact, Notification). Provides comprehensive guidance for creating and implementing Claude Code plugin hooks with focus on advanced prompt-based hooks API.
typescript-best-practices
by aiskillstore
Provides TypeScript patterns for type-first development, making illegal states unrepresentable, exhaustive handling, and runtime validation. Must use when reading or writing TypeScript/JavaScript files.
by phodal
Extract and analyze information from PDF documents
deseq2-differential-expression
by jaechang-hits
"Differential expression analysis for bulk RNA-seq using R/Bioconductor DESeq2. Negative binomial GLM with empirical Bayes shrinkage, Wald and LRT tests, multi-factor designs, interaction terms, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap visualization. The R gold standard for DE analysis with native Bioconductor integration. Use pydeseq2-differential-expression for Python-based pipelines; use edgeR for TMM normalization."
nnunet-segmentation
by jaechang-hits
"Train and deploy automated medical image segmentation models using nnU-Net's self-configuring framework that auto-selects optimal architecture, preprocessing, and training for any modality. Supports CT, MRI, microscopy, and ultrasound with 2D, 3D full-res, 3D low-res, and cascade configurations. Pipeline: convert dataset → plan and preprocess → train (5-fold cross-validation) → find best configuration → predict → ensemble. Use when classical segmentation fails and annotated training data is available."
scikit-survival-analysis
by jaechang-hits
"Survival analysis and time-to-event modeling with scikit-survival. Cox proportional hazards (standard/elastic net), Random Survival Forests, Gradient Boosting, SVMs for censored data. C-index (Harrell/Uno), Brier score, time-dependent AUC evaluation. Kaplan-Meier, Nelson-Aalen, competing risks. scikit-learn Pipeline/GridSearchCV compatible. For frequentist regression use statsmodels; for Bayesian survival use pymc; for simpler parametric models use lifelines."
figma-implement-design
by Kilo-Org
"Translate Figma nodes into production-ready code with 1:1 visual fidelity using the Figma MCP workflow (design context, screenshots, assets, and project-convention translation). Trigger when the user provides Figma URLs or node IDs, or asks to implement designs or components that must match Figma specs. Requires a working Figma MCP server connection."
venture-financing
by open-agreements
Draft and fill NVCA model documents — stock purchase agreement, certificate of incorporation, investors rights agreement, voting agreement, ROFR, co-sale, indemnification, management rights letter. Series A and venture financing templates. Produces signable DOCX files.
nda
by open-agreements
Draft and fill NDA templates — mutual NDA, one-way NDA, confidentiality agreement. Produces signable DOCX files from Common Paper and Bonterms standard forms.
pydicom-medical-imaging
by jaechang-hits
"Pure Python DICOM library for medical imaging (CT, MRI, X-ray, ultrasound). Read/write DICOM files, extract pixel data as NumPy arrays, access/modify metadata tags, apply windowing (VOI LUT), anonymize PHI, build DICOM from scratch, process series into 3D volumes. For whole-slide pathology images use histolab; for NIfTI neuroimaging use nibabel."
ena-database
by jaechang-hits
"European Nucleotide Archive (ENA) REST API access for genomic sequences, raw reads, assemblies, and annotations. Portal API search with query syntax, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM download URLs, taxonomy queries, cross-references. For multi-database Python queries prefer bioservices; for NCBI-specific queries use pubmed-database or Biopython Entrez."
miro-mcp
by miroapp
This skill teaches how to use Miro MCP tools effectively for creating diagrams, documents, tables, and extracting context from Miro boards. Use when the user asks about Miro capabilities, wants to create content on Miro boards, or needs to work with Miro board data.
archs4-database
by jaechang-hits
"Query uniformly processed RNA-seq gene expression profiles, tissue-specific expression patterns, and co-expression networks from the ARCHS4 database REST API. Retrieve z-score normalized expression across 1M+ human and mouse samples, find co-expressed genes, search samples by metadata, and download HDF5 expression matrices. For variant-level population genetics use gnomad-database; for pathway enrichment from gene lists use gget-genomic-databases (Enrichr)."
audience-synthesis
by jmagly
Data sources: .aiwg/marketing/config/data-sources.yaml