Topic: skills
17,247 skills in this topic.
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gwas-database
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
x-cmd/skill 19
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gtars
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
x-cmd/skill 19
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pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
x-cmd/skill 19
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scientific-critical-thinking
Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.
x-cmd/skill 19
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protocolsio-integration
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
x-cmd/skill 19
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kegg-database
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
x-cmd/skill 19
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scientific-brainstorming
Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation.
x-cmd/skill 19
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neuropixels-analysis
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
x-cmd/skill 19
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qutip
Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.
x-cmd/skill 19
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pymc-bayesian-modeling
Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
x-cmd/skill 19
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pymatgen
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
x-cmd/skill 19
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uspto-database
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
x-cmd/skill 19
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bun
High-performance JavaScript runtime and package manager module. Core Scenario: When the user needs an extremely fast JS/TS runtime or package manager for local development.
x-cmd/skill 19
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deno
Enhanced Deno module for running modern JavaScript and TypeScript with zero setup. Core Scenario: When the user needs to execute TypeScript scripts or manage Deno-based applications.
x-cmd/skill 19
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nu
Enhanced interface for Nushell, enabling x-cmd integration, documentation search, and AI-powered command generation. Core Scenario: When the user needs to set up x-cmd in Nushell or search Nushell documentation via CLI.
x-cmd/skill 19
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mankier
Command-line client for ManKier.com, offering manual page queries and detailed command explanation. Core Scenario: When the user needs to explain shell commands or fetch specific sections of online manual pages.
x-cmd/skill 19
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gemini
Integrate Google Gemini AI for chat, text analysis, and multimodal tasks like image understanding. Core Scenario: When the user wants to use Gemini models for advanced chat, translation with file context, or analyzing images via CLI.
x-cmd/skill 19
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npx
Enhanced interface for npx, used to execute Node.js packages without local installation. Core Scenario: When the user needs to run a one-off Node.js tool or test a package.
x-cmd/skill 19
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hi
Display detailed HTTP information and network metadata. Core Scenario: When the user needs a quick summary of their current HTTP environment or request headers.
x-cmd/skill 19
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dingtalk
Send messages to DingTalk groups using bot webhooks, supporting Markdown and interactive cards. Core Scenario: When the user needs to automate notifications or send interactive messages to a DingTalk group.
x-cmd/skill 19
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pkgx
Universal tool runner for executing any open-source tool without pre-installation or config. Core Scenario: When the user needs to run a CLI tool instantly without modifying their system or PATH.
x-cmd/skill 19
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sed
Enhanced stream editor with interactive preview of search and replace operations using FZF. Core Scenario: When the user needs to perform text substitutions and wants to see the effects before applying changes.
x-cmd/skill 19
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rg
Modern, high-speed line-oriented search tool (ripgrep) with an interactive FZF interface. Core Scenario: When the user needs to perform recursive text searches in large codebases or directories.
x-cmd/skill 19
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uname
Enhanced system information display with structured key-value output. Core Scenario: When the user needs a quick, readable summary of kernel version, architecture, and OS name.
x-cmd/skill 19