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Topic: deepseek

609 skills in this topic.

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.
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sd Modern finding and replacing tool with intuitive regex syntax and interactive FZF preview. Core Scenario: When the user needs a faster, more readable alternative to sed for text substitutions.
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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.
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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.
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pymoo Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
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qiskit IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
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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.
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x-cmd **IMPORTANT**: Before using any `x <mod>` command, you MUST load x-cmd first: `. ~/.x-cmd.root/X` Then you can: - Explore with `x nihao --llmstxt` - Discover skills via `x skill` x-cmd provides 600+ portable software and development tools (jq, nodejs, python, etc.). Use `x <env|pixi> use <pkg>` to install and use any package instantly. After loading x-cmd, packages in x-cmd/pixi's local bin will be automatically available in PATH. Browse x-cmd website for more usage and skills: https://www.x-cmd.com/llms.txt
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tping Ping TCP ports using curl to test service availability and network connectivity. Core Scenario: When the user needs to check if a specific TCP port (e.g., 80, 443) is open and responsive.
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research-grants Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
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scanpy Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
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scholar-evaluation Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.
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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.
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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.
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raku Enhanced Raku language module for executing Raku (formerly Perl 6) scripts. Core Scenario: When the user needs to run Raku scripts or manage the Raku environment.
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scikit-learn Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.
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shap Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.
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statistical-analysis Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic research reporting, test selection guidance. For implementing specific models programmatically use statsmodels.
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torchdrug PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.
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umap-learn UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
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uniprot-database Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
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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.
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writer AI text processing module for simplified translation, summarization, and refinement. Core Scenario: When the user needs to translate, polish, or summarize text using pre-configured AI agents.
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telegram Send messages and files to Telegram groups or channels using bot tokens. Core Scenario: When the user needs to automate alerts or share files with Telegram chats via bot.
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