Agent Skills Directory

Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.

World-class senior data scientist skill specialising in statistical modeling, experiment design, causal inference, and predictive analytics. Covers A/B testing (sample sizing, two-proportion z-tests, Bonferroni correction), difference-in-differences, feature engineering pipelines (Scikit-learn, XGBoost), cross-validated model evaluation (AUC-ROC, AUC-PR, SHAP), and MLflow experiment tracking — using Python (NumPy, Pandas, Scikit-learn), R, and SQL. Use when designing or analysing controlled experiments, building and evaluating classification or regression models, performing causal analysis on observational data, engineering features for structured tabular datasets, or translating statistical findings into data-driven business decisions.

Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.

Comprehensive DevOps skill for CI/CD, infrastructure automation, containerization, and cloud platforms (AWS, GCP, Azure). Includes pipeline setup, infrastructure as code, deployment automation, and monitoring. Use when setting up pipelines, deploying applications, managing infrastructure, implementing monitoring, or optimizing deployment processes.

Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are connected, or surveying available analysis skills before starting a new project.

Two-layer memory architecture for board meeting decisions. Manages raw transcripts (Layer 1) and approved decisions (Layer 2). Use when logging decisions after a board meeting, reviewing past decisions with /cs:decisions, or checking overdue action items with /cs:review. Invoked automatically by the board-meeting skill after Phase 5 founder approval.

Package an escalation for engineering, product, or leadership with full context. Use when a bug needs engineering attention beyond normal support, multiple customers report the same issue, a customer is threatening to churn, or an issue has sat unresolved past its SLA.

Multi-source research on a customer question or topic with source attribution. Use when a customer asks something you need to look up, investigating whether a bug has been reported before, checking what was previously told to a specific account, or gathering background before drafting a response.

Draft a knowledge base article from a resolved issue or common question. Use when a ticket resolution is worth documenting for self-service, the same question keeps coming up, a workaround needs to be published, or a known issue should be communicated to customers.

ML engineering skill for productionizing models, building MLOps pipelines, and integrating LLMs. Covers model deployment, feature stores, drift monitoring, RAG systems, and cost optimization. Use when the user asks about deploying ML models to production, setting up MLOps infrastructure (MLflow, Kubeflow, Kubernetes, Docker), monitoring model performance or drift, building RAG pipelines, or integrating LLM APIs with retry logic and cost controls. Focused on production and operational concerns rather than model research or initial training.

Triage and prioritize a support ticket or customer issue. Use when a new ticket comes in and needs categorization, assigning P1-P4 priority, deciding which team should handle it, or checking whether it's a duplicate or known issue before routing.

Answer data questions -- from quick lookups to full analyses. Use when looking up a single metric, investigating what's driving a trend or drop, comparing segments over time, or preparing a formal data report for stakeholders.