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.

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.

Advanced Scrum Master skill for data-driven agile team analysis and coaching. Use when the user asks about sprint planning, velocity tracking, retrospectives, standup facilitation, backlog grooming, story points, burndown charts, blocker resolution, or agile team health. Runs Python scripts to analyse sprint JSON exports from Jira or similar tools: velocity_analyzer.py for Monte Carlo sprint forecasting, sprint_health_scorer.py for multi-dimension health scoring, and retrospective_analyzer.py for action-item and theme tracking. Produces confidence-interval forecasts, health grade reports, and improvement-velocity trends for high-performing Scrum teams.

This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate decision trees, or get help choosing what scientific problem to work on. Typical requests include "I have an idea for a project", "I'm stuck on my research", "help me evaluate this project", "what should I work on", or "I need strategic advice about my research".

Plan resource capacity — workload analysis and utilization forecasting. Use when heading into quarterly planning, the team feels overallocated and you need the numbers, deciding whether to hire or deprioritize, or stress-testing whether upcoming projects fit the people you have.

Atlassian Jira expert for creating and managing projects, planning, product discovery, JQL queries, workflows, custom fields, automation, reporting, and all Jira features. Use for Jira project setup, configuration, advanced search, dashboard creation, workflow design, and technical Jira operations.

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.

/em -challenge — Pre-Mortem Plan Analysis

Senior Project Manager for enterprise software, SaaS, and digital transformation projects. Specializes in portfolio management, quantitative risk analysis, resource optimization, stakeholder alignment, and executive reporting. Uses advanced methodologies including EMV analysis, Monte Carlo simulation, WSJF prioritization, and multi-dimensional health scoring. Use when a user needs help with project plans, project status reports, risk assessments, resource allocation, project roadmaps, milestone tracking, team capacity planning, portfolio health reviews, program management, or executive-level project reporting — especially for enterprise-scale initiatives with multiple workstreams, complex dependencies, or multi-million dollar budgets.

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.

/em -postmortem — Honest Analysis of What Went Wrong

Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.