File Ops
File manipulation and management
web-search-advanced-personal-site
by exa-labs
Search personal websites and blogs using Exa advanced search. Full filter support for finding individual perspectives, portfolios, and personal blogs. Use when searching for personal sites, blog posts, or portfolio websites.
web-search-advanced-research-paper
by exa-labs
Search for research papers and academic content using Exa advanced search. Full filter support including date ranges and text filtering. Use when searching for academic papers, arXiv preprints, or scientific research.
AI Feedback Reporter
by HoangNguyen0403
CRITICAL - Before ANY file write, audit loaded skills for violations. Auto-report via feedback command.
Bun Runtime
by secondsky
Use for Bun runtime, bunfig.toml, watch/hot modes, env vars, CLI flags, and module resolution.
python-dev
by databricks-solutions
"Python development guidance with code quality standards, error handling, testing practices, and environment management. Use when writing, reviewing, or modifying Python code (.py files) or Jupyter notebooks (.ipynb files)."
openspec-ff-change
by rivet-dev
Fast-forward through OpenSpec artifact creation. Use when the user wants to quickly create all artifacts needed for implementation without stepping through each one individually.
openspec-archive-change
by rivet-dev
Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.
openspec-ff-change
by rivet-dev
Fast-forward through OpenSpec artifact creation. Use when the user wants to quickly create all artifacts needed for implementation without stepping through each one individually.
openspec-sync-specs
by rivet-dev
Sync delta specs from a change to main specs. Use when the user wants to update main specs with changes from a delta spec, without archiving the change.
openspec-archive-change
by rivet-dev
Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.
openspec-sync-specs
by rivet-dev
Sync delta specs from a change to main specs. Use when the user wants to update main specs with changes from a delta spec, without archiving the change.
tooluniverse-network-pharmacology
by mims-harvard
Construct and analyze compound-target-disease networks for drug repurposing, polypharmacology discovery, and systems pharmacology. Builds multi-layer networks from ChEMBL, OpenTargets, STRING, DrugBank, Reactome, FAERS, and 60+ other ToolUniverse tools. Calculates Network Pharmacology Scores (0-100), identifies repurposing candidates, predicts mechanisms, and analyzes polypharmacology. Use when users ask about drug repurposing via network analysis, multi-target drug effects, compound-target-disease networks, systems pharmacology, or polypharmacology.
tooluniverse-chemical-compound-retrieval
by mims-harvard
Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment. Creates comprehensive compound profiles with identifiers, properties, bioactivity, and drug information. Use when users need chemical data, drug information, or mention PubChem CID, ChEMBL ID, SMILES, InChI, or compound names.
tooluniverse-multiomic-disease-characterization
by mims-harvard
Comprehensive multi-omics disease characterization integrating genomics, transcriptomics, proteomics, pathway, and therapeutic layers for systems-level understanding. Produces a detailed multi-omics report with quantitative confidence scoring (0-100), cross-layer gene concordance analysis, biomarker candidates, therapeutic opportunities, and mechanistic hypotheses. Uses 80+ ToolUniverse tools across 8 analysis layers. Use when users ask about disease mechanisms, multi-omics analysis, systems biology of disease, biomarker discovery, or therapeutic target identification from a disease perspective.
tooluniverse-cancer-variant-interpretation
by mims-harvard
Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR L858R, BRAF V600E) and optional cancer type, performs multi-database analysis covering clinical evidence (CIViC), mutation prevalence (cBioPortal), therapeutic associations (OpenTargets, ChEMBL, FDA), resistance mechanisms, clinical trials, prognostic impact, and pathway context. Generates an evidence-graded markdown report with actionable recommendations for precision oncology. Use when oncologists, molecular tumor boards, or researchers ask about treatment options for specific cancer mutations, resistance mechanisms, or clinical trial matching.
tooluniverse-antibody-engineering
by mims-harvard
Comprehensive antibody engineering and optimization for therapeutic development. Covers humanization, affinity maturation, developability assessment, and immunogenicity prediction. Use when asked to optimize antibodies, humanize sequences, or engineer therapeutic antibodies from lead to clinical candidate.
tooluniverse-literature-deep-research
by mims-harvard
Conduct comprehensive literature research with target disambiguation, evidence grading, and structured theme extraction. Creates a detailed report with mandatory completeness checklist, biological model synthesis, and testable hypotheses. For biological targets, resolves official IDs (Ensembl/UniProt), synonyms, naming collisions, and gathers expression/pathway context before literature search. Default deliverable is a report file; for single factoid questions, uses a fast verification mode and may include an inline answer. Use when users need thorough literature reviews, target profiles, or to verify specific claims from the literature.
filesystem
by Mathews-Tom
'File and directory operations via Claude Code built-in tools, replacing the Filesystem MCP server. Triggers on: "read this file", "write to file", "edit file", "find files matching", "search for text in files", "list directory", "show directory tree", "rename file".'
arXiv Preflight Check
by Mathews-Tom
Curated, production-grade skills for AI coding agents. Battle-tested workflows for developers who use AI seriously.
watch
by Mathews-Tom
'Use when analyzing an existing video URL or local recording: "watch this video", "analyze youtube video", "summarize this video", "youtube transcript", "find this moment", "what happens on screen", "extract concepts from video", or "video key points". NOT for finding videos by keyword (use youtube-search) or creating videos (use concept-to-video or remotion-video).'
skill-development
by fcakyon
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.
bmad-os-audit-file-refs
by bmad-code-org
Audit BMAD source files for file-reference convention violations using parallel Haiku subagents. Use when users requests an "audit file references" for a skill, workflow or task.
bd-to-br-migration
by Dicklesworthstone
Migrate docs from bd (beads) to br (beads_rust). Use when updating AGENTS.md, converting bd commands, "bd sync" → "br sync --flush-only", or beads migration.
context-manager
by darrenhinde
Context management skill providing discovery, fetching, harvesting, extraction, compression, organization, cleanup, and guided workflows for project context