Agent Skills Directory

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.

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.

Cross-functional what-if modeling for cascading multi-variable scenarios. Unlike single-assumption stress testing, this models compound adversity across all business functions simultaneously. Use when facing complex risk scenarios, strategic decisions with major downside, or when the user asks 'what if X AND Y both happen?'

When the user wants to design, launch, or optimize a referral or affiliate program. Use when they mention 'referral program,' 'affiliate program,' 'word of mouth,' 'refer a friend,' 'incentive program,' 'customer referrals,' 'brand ambassador,' 'partner program,' 'referral link,' or 'growth through referrals.' Covers program mechanics, incentive design, and optimization — not just the idea of referrals but the actual system.

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.

International market expansion strategy. Market selection, entry modes, localization, regulatory compliance, and go-to-market by region. Use when expanding to new countries, evaluating international markets, planning localization, or building regional 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".

Systematic competitor tracking that feeds CMO positioning, CRO battlecards, and CPO roadmap decisions. Use when analyzing competitors, building sales battlecards, tracking market moves, positioning against alternatives, or when user mentions competitive intelligence, competitive analysis, competitor research, battlecards, win/loss, or market positioning.

SaaS financial health advisor. Use when a user shares revenue or customer numbers, or mentions ARR, MRR, churn, LTV, CAC, NRR, or asks how their SaaS business is doing.

Contract & Proposal Writer

/em -stress-test — Business Assumption Stress Testing

Design, optimize, and communicate SaaS pricing — tier structure, value metrics, pricing pages, and price increase strategy. Use when building a pricing model from scratch, redesigning existing pricing, planning a price increase, or improving a pricing page. Trigger keywords: pricing tiers, pricing page, price increase, packaging, value metric, per seat pricing, usage-based pricing, freemium, good-better-best, pricing strategy, monetization, pricing page conversion, Van Westendorp. NOT for broader product strategy — use product-strategist for that. NOT for customer success or renewals — use customer-success-manager for expansion revenue.