Agent Skills Directory

Identify, categorize, and prioritize technical debt. Trigger with "tech debt", "technical debt audit", "what should we refactor", "code health", or when the user asks about code quality, refactoring priorities, or maintenance backlog.

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.

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.

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.

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.

When the user wants to write, improve, or build a sequence of B2B cold outreach emails to prospects who haven't asked to hear from them. Use when the user mentions 'cold email,' 'cold outreach,' 'prospecting emails,' 'SDR emails,' 'sales emails,' 'first touch email,' 'follow-up sequence,' or 'email prospecting.' Also use when they share an email draft that sounds too sales-y and needs to be humanized. Distinct from email-sequence (lifecycle/nurture to opted-in subscribers) — this is unsolicited outreach to new prospects. NOT for lifecycle emails, newsletters, or drip campaigns (use email-sequence).

Incident Commander Skill