148 ready-to-use AI agent skills for research, science, engineering, analysis & writing. Works with Claude Code, Cursor, Codex and any Agent Skills-compatible agent.
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick…
Lord1Egypt/scientific-agent-toolkit
Skill Claude Code
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
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…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive plots use plotly; for publication styling use…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
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…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.
Lord1Egypt/scientific-agent-toolkit
Skill Claude Code
Spatial transcriptomics data analysis with Squidpy, SpatialDE, and MERFISH/Visium/Xenium workflows. Use for spatial gene expression analysis, neighborhood enrichment, spatial variable gene detection, cell-cell communication with spatial context, and tissue domain identification. Complements Scanpy for…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments. For high-performance parallel training, multi-agent…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
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…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series, rigorous inference with coefficient tables. For guided statistical test selection with APA reporting use…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.
Lord1Egypt/scientific-agent-toolkit
Skill Claude Code
Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction intervals. Includes a preflight system checker script to verify…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Guide for building Graph Neural Networks with PyTorch Geometric (PyG). Use this skill whenever the user asks about graph neural networks, GNNs, node classification, link prediction, graph classification, message passing networks, heterogeneous graphs, neighbor sampling, or any task involving torchgeometric / PyG. Also…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
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…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning…
Lord1Egypt/scientific-agent-toolkit
Skill Claude Code
Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Query the U.S. Treasury Fiscal Data API for federal financial data including national debt, government spending, revenue, interest rates, exchange rates, and savings bonds. Access 54 datasets and 182 data tables with no API key required. Use when working with U.S. federal fiscal data, national debt tracking (Debt to…
Lord1Egypt/scientific-agent-toolkit
Skill Claude CodeCodex
Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: