File Ops
File manipulation and management
bio-alignment-io
by GPTomics
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
bio-atac-seq-atac-peak-calling
by GPTomics
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
bio-virtual-screening
by GPTomics
Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files, generates ligand conformers, defines binding site boxes, and ranks compounds by predicted binding affinity. Use when screening chemical libraries against a protein structure to find potential binders.
bio-substructure-search
by GPTomics
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matches with atom mapping. Use when finding compounds containing specific chemical moieties or filtering libraries by structural features.
bio-causal-genomics-fine-mapping
by GPTomics
Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.
tavily-crawl
by tavily-ai
Crawl websites and extract content from multiple pages via the Tavily CLI. Use this skill when the user wants to crawl a site, download documentation, extract an entire docs section, bulk-extract pages, save a site as local markdown files, or says "crawl", "get all the pages", "download the docs", "extract everything under /docs", "bulk extract", or needs content from many pages on the same domain. Supports depth/breadth control, path filtering, semantic instructions, and saving each page as a local markdown file.
sales-council
by antonioc-cl
Expert sales council with 6 advisors (Cialdini, Hormozi, Rackham, Voss, Klaff, Schwartz) for pricing, persuasion, negotiation, copywriting, and pitch strategies.
tavily-research
by tavily-ai
Conduct comprehensive AI-powered research with citations via the Tavily CLI. Use this skill when the user wants deep research, a detailed report, a comparison, market analysis, literature review, or says "research", "investigate", "analyze in depth", "compare X vs Y", "what does the market look like for", or needs multi-source synthesis with explicit citations. Returns a structured report grounded in web sources. Takes 30-120 seconds. For quick fact-finding, use tavily-search instead.
tavily-search
by tavily-ai
Search the web with LLM-optimized results via the Tavily CLI. Use this skill when the user wants to search the web, find articles, look up information, get recent news, discover sources, or says "search for", "find me", "look up", "what's the latest on", "find articles about", or needs current information from the internet. Returns relevant results with content snippets, relevance scores, and metadata — optimized for LLM consumption. Supports domain filtering, time ranges, and multiple search depths.
tavily-best-practices
by tavily-ai
"Build production-ready Tavily integrations with best practices baked in. Reference documentation for developers using coding assistants (Claude Code, Cursor, etc.) to implement web search, content extraction, crawling, and research in agentic workflows, RAG systems, or autonomous agents."
search
by tavily-ai
"Search the web using Tavily's LLM-optimized search API. Returns relevant results with content snippets, scores, and metadata. Use when you need to find web content on any topic without writing code."
dashboard-create-screen
by Automattic
Create a new screen in the Multi-site Dashboard with automatic route registration
aws-sdk-java-v2-s3
by giuseppe-trisciuoglio
Provides Amazon S3 patterns and examples using AWS SDK for Java 2.x. Use when working with S3 buckets, uploading/downloading objects, multipart uploads, presigned URLs, S3 Transfer Manager, object operations, or S3-specific configurations.
chunking-strategy
by giuseppe-trisciuoglio
Provides optimal chunking strategies in RAG systems and document processing pipelines. Use when building retrieval-augmented generation systems, vector databases, or processing large documents that require breaking into semantically meaningful segments for embeddings and search.
too-long-skill
by pproenca
This skill has more than 500 lines which should fail validation.
missing-references
by pproenca
This skill references rules that do not have corresponding files in the references directory.
elixir-essentials
by j-morgan6
MANDATORY for ALL Elixir code changes. Invoke before writing any .ex or .exs file.
stacks-marketing-directory-submissions
by stacksjs
Use when the user wants to submit their product to startup, SaaS, AI, agent, MCP, no-code, or review directories for backlinks, domain rating, and discovery. Covers marketing planning and its Stacks implementation.
stacks-logging
by stacksjs
Use when implementing logging in Stacks - the log facade (info, error, warn, debug, success), dump/dd debugging, timing functions, file-based logging, or log configuration. Covers @stacksjs/logging and config/logging.ts.
stacks-marketing-copy-editing
by stacksjs
Use when the user wants to edit, review, or improve existing marketing copy, or refresh outdated content. Covers marketing planning and its Stacks implementation.
ecto-essentials
by j-morgan6
MANDATORY for ALL database work. Invoke before modifying schemas, queries, or migrations.
symfony:symfony-messenger
by MakFly
Implement resilient Symfony async workflows with idempotency, retries, and operational visibility. Use for symfony messenger tasks.
standards
by boshu2
'Language-specific coding standards and validation rules. Provides Python, Go, Rust, TypeScript, Shell, YAML, JSON, and Markdown standards. Auto-loaded by /vibe, /implement, /doc, /bug-hunt, /complexity based on file types.'
converter
by boshu2
'Cross-platform skill converter. Parse AgentOps skills into a universal bundle format, then convert to target platforms (Codex, Cursor). Triggers: convert, converter, convert skill, export skill, cross-platform.'