This skill should be used when the user asks about "plugin settings", "store plugin configuration", "user-configurable plugin", ".local.md files", "plugin state files", "read YAML frontmatter", "per-project plugin settings", or wants to make plugin behavior configurable. Documents the .claude/plugin-name.local.md pattern for storing plugin-specific configuration with YAML frontmatter and markdown content.
This skill should be used when the user asks to "create a plugin", "scaffold a plugin", "understand plugin structure", "organize plugin components", "set up plugin.json", "use ${CLAUDE_PLUGIN_ROOT}", "add commands/agents/skills/hooks", "configure auto-discovery", or needs guidance on plugin directory layout, manifest configuration, component organization, file naming conventions, or Claude Code plugin architecture best practices.
This skill should be used when the user wants to "create a skill", "add a skill to plugin", "write a new skill", "improve skill description", "organize skill content", or needs guidance on skill structure, progressive disclosure, or skill development best practices for Claude Code plugins.
Generate and publish a project status artifact — an opinionated, tabbed status page for a project too big for one update (overview & success criteria, the workstream sequence, next steps, plus background, plan, risks & open questions, and decisions/FAQ when they earn a tab) — published with the built-in Artifact tool to a default-private claude.ai page the user can share with teammates. Use when a piece of work spans several workstreams and you want a shareable overview kept current. Each artifact is backed by a small per-project config in the plugin data dir, so refreshing it re-gathers live state, redeploys the same URL, and reports only the delta. For software projects whose workstreams are PRs, also read swe.md (the X.Y PR-numbering convention; pulling PR state with gh/git; a per-PR detail block). Needs the built-in Artifact tool (claude.ai login). Not for single-PR changes or public docs.
Generate a personal Claude Code usage & impact report ("receipts") from this machine's local session transcripts — for justifying Claude Code usage/spend to a manager, self-review, or "what have I been using this for" check-ins. Mines ~/.claude/projects locally (no extra API calls beyond one final write-up), cross-references local git history, and writes a markdown report plus a self-contained HTML receipt to your home directory. Use when the user asks for "receipts", an "impact report", "usage report", wants to "show my Claude Code activity", "prove the value of Claude Code", or runs `/receipts`.
Generate an explorable HTML report of Claude Code session usage (tokens, cache, subagents, skills, expensive prompts) from ~/.claude/projects transcripts.
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full ASM JSON, flattened CSV for easy import, and exportable Python code for data engineers. Common triggers include converting instrument files, standardizing lab data, preparing data for upload to LIMS/ELN systems, or generating parser code for production pipelines.
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.
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".
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.
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.
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.
Customize a Claude Code plugin for a specific organization's tools and workflows. Use when: customize plugin, set up plugin, configure plugin, tailor plugin, adjust plugin settings, customize plugin connectors, customize plugin skill, tweak plugin, modify plugin configuration.
Guide users through creating a new plugin from scratch in a cowork session. Use when users want to create a plugin, build a plugin, make a new plugin, develop a plugin, scaffold a plugin, start a plugin from scratch, or design a plugin. This skill requires Cowork mode with access to the outputs directory for delivering the final .plugin file.
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 professional customer-facing response tailored to the situation and relationship. Use when answering a product question, responding to an escalation or outage, delivering bad news like a delay or won't-fix, declining a feature request, or replying to a billing issue.
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.
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.
A folder with a SKILL.md file: a name, a description of when to use it, and instructions. Claude loads a skill only when the task matches its description.
How do I use one I find here?
Copy the folder into your project's .claude/skills/ directory, or into your own skills folder to use it everywhere.
What do the warnings mean?
We read each file for commands that read secrets, delete things or pipe downloads into a shell, and say so before you copy it. No warning is not a promise that a file is safe.
Which skills worked for people?
Open a skill to see its discussion. Reports from people and their agents are coming.
AnthropicSkill