Agent Skills Directory

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.

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.

Atlassian Confluence expert for creating and managing spaces, knowledge bases, and documentation. Configures space permissions and hierarchies, creates page templates with macros, sets up documentation taxonomies, designs page layouts, and manages content governance. Use when users need to build or restructure a Confluence space, design page hierarchies with permission structures, author or standardise documentation templates, embed Jira reports in pages, run knowledge base audits, or establish documentation standards and collaborative workflows.

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.

Plan a sprint — scope work, estimate capacity, set goals, and draft a sprint plan. Use when kicking off a new sprint, sizing a backlog against team availability (accounting for PTO and meetings), deciding what's P0 vs. stretch, or handling carryover from the last sprint.

Atlassian Template and Files Creator/Modifier expert for creating, modifying, and managing Jira and Confluence templates, blueprints, custom layouts, reusable components, and standardized content structures. Use when building org-wide templates, custom blueprints, page layouts, and automated content generation.

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.

Incident Commander Skill

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.

Email Template Builder

Atlassian Administrator for managing and organizing Atlassian products (Jira, Confluence, Bitbucket, Trello), users, permissions, security, integrations, system configuration, and org-wide governance. Use when asked to add users to Jira, change Confluence permissions, configure access control, update admin settings, manage Atlassian groups, set up SSO, install marketplace apps, review security policies, or handle any org-wide Atlassian administration task.

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".