File Ops
File manipulation and management
tooluniverse-protein-structure-retrieval
by mims-harvard
Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles. Creates detailed structure reports with experimental metadata, ligand information, and download links. Use when users need protein structures, 3D models, crystallography data, or mention PDB IDs (4-character codes like 1ABC) or UniProt accessions.
gemini-interactions-api
by google-gemini
Use this skill when writing code that calls the Gemini API for text generation, multi-turn chat, multimodal understanding, image generation, streaming responses, background research tasks, function calling, structured output, or migrating from the old generateContent API. This skill covers the Interactions API, the recommended way to use Gemini models and agents in Python and TypeScript.
winuae-amiberry-merge
by BlitterStudio
Assist with merging updates and synchronizing functionality from the upstream WinUAE repository (Windows) to Amiberry (Linux/macOS/Android/Windows). Includes a comprehensive guide for porting Win32 GUI dialogs to Dear ImGui, mapping Windows controls to ImGui equivalents, and analyzing platform-specific code. Use this for analyzing upstream commits, identifying Windows-specific code, adapting GUI panels, and verifying feature parity.
plugin-structure
by fcakyon
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.
plugin-settings
by fcakyon
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.
paper-search-usage
by fcakyon
This skill should be used when user asks to "search for papers", "find research papers", "search arXiv", "search PubMed", "find academic papers", "search IEEE", "search Scopus", or "look up scientific literature".
setup
by fcakyon
This skill should be used when user encounters "paper-search MCP error", "Docker not found", "Docker not running", "paper search not working", or needs help configuring paper search integration.
slack-usage
by fcakyon
This skill should be used when user asks to "search Slack for messages", "find Slack messages about X", "get channel history", "look up conversation in Slack", or "find what someone said in Slack".
tooluniverse-expression-data-retrieval
by mims-harvard
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports. Creates comprehensive dataset profiles with metadata, sample information, and download links. Use when users need expression data, omics datasets, or mention ArrayExpress (E-MTAB, E-GEOD) or BioStudies (S-BSST) accessions.
tooluniverse-drug-drug-interaction
by mims-harvard
Comprehensive drug-drug interaction (DDI) prediction and risk assessment. Analyzes interaction mechanisms (CYP450, transporters, pharmacodynamic), severity classification, clinical evidence grading, and provides management strategies. Supports single drug pairs, polypharmacy analysis (3+ drugs), and alternative drug recommendations. Use when users ask about drug interactions, medication safety, polypharmacy risks, or need DDI assessment for clinical decision support.
xlsx
by snyk
"Comprehensive spreadsheet creation, editing, and analysis with support for formulas, formatting, data analysis, and visualization. When Claude needs to work with spreadsheets (.xlsx, .xlsm, .csv, .tsv, etc) for: (1) Creating new spreadsheets with formulas and formatting, (2) Reading or analyzing data, (3) Modify existing spreadsheets while preserving formulas, (4) Data analysis and visualization in spreadsheets, or (5) Recalculating formulas"
hyprland
by marceloeatworld
This skill should be used when the user asks about "Hyprland configuration", "hyprland.conf", "hyprctl", "Hyprland keybinds", "Hyprland window rules", "Hyprland monitors", "Hyprland dispatchers", "Hyprland animations", "Hyprland workspaces", "Hyprland IPC", "Hyprland plugins", "hyprlock", "hypridle", "hyprpaper", "hyprcursor", "hyprpicker", "hyprsunset", "xdg-desktop-portal-hyprland", "Hyprland on NixOS", "Hyprland Home Manager", "Hyprland layouts", "Hyprland dwindle", "Hyprland master layout", "Hyprland FAQ", "Hyprland performance", "Hyprland Nvidia", "Hyprland screen sharing", "Hyprland special workspace", "Hyprland smart gaps", "Hyprland multi-monitor", "Hyprland tearing", or any topic related to configuring, troubleshooting, or extending the Hyprland Wayland compositor and its ecosystem tools.
paper-reader
by huangkiki
Use when user asks to "read paper", "analyze paper", "summarize paper", "读论文", "分析文献", "帮我看一下这篇paper", "论文笔记", or provides a PDF file that appears to be an academic paper. Specialized for CV/DL papers. Also supports Zotero integration: "读一下这篇论文 ...", "快速看一下这篇论文 ...", "批判性分析这篇论文 ...", "读一下 Zotero 里的 XXX", "批量读一下 Zotero 里 VLA 分类下的论文" 重要触发词: "读一下 XXX"、"读一下这篇"、"帮我读" → 必须调用此 skill
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.
structural-search
by 0xDarkMatter
"Search code by AST structure using ast-grep. Find semantic patterns like function calls, imports, class definitions instead of text patterns. Triggers on: find all calls to X, search for pattern, refactor usages, find where function is used, structural search, ast-grep, sg."
read-docs
by fuma-nama
Enables efficient, accurate retrieval of content from Fumadocs-powered documentation sites.
make-skill
by dotnet
'Create new Agent Skills for GitHub Copilot. Use when asked to create, scaffold, or add a skill. Generates SKILL.md with frontmatter, directory structure, and optional resources.'
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.