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- Skillxlsx
### Xlsx - name: "xlsx" - description: "Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet…
- Skillzarr-python
### Zarr Python - name: "zarr-python" - description: "Chunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, parallel I/O, S3/GCS via fsspec, NumPy/Dask/Xarray compatible, for large-scale scientific co…
- Skillscvi-tools
### Scvi Tools - name: "scvi-tools" - description: "Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or…
- Skillwhat-if-oracle
### What If Oracle - name: "what-if-oracle" - description: "Run structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order). Use when the user…
- Skillusfiscaldata
### Usfiscaldata - name: "usfiscaldata" - description: "Query the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (Debt to the Penny), Daily Treasury Statements,…
- Skillvaex
### Vaex - name: "vaex" - description: "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,…
- Skillvenue-templates
### Venue Templates - name: "venue-templates" - description: "Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE…
- Skillscikit-bio
### Scikit Bio - name: "scikit-bio" - description: "Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, fo…
- Skillscientific-writing
### Scientific Writing - name: "scientific-writing" - description: "Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1…
- Skillsimpy
### Simpy - name: "simpy" - description: "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…
- Skillumap-learn
### Umap Learn - name: "umap-learn" - description: "UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimen…
- Skilltreatment-plans
### Treatment Plans - name: "treatment-plans" - description: "Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilita…
- Skillstatsmodels
### Statsmodels - name: "statsmodels" - description: "Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference.…
- Skilltiledbvcf
### Tiledbvcf - name: "tiledbvcf" - description: "Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and…
- Skillsympy
### Sympy - name: "sympy" - description: "Use when you need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or code generation via lambdify/LaTeX. Prefer NumPy or SciPy when…
- Skilltransformers
### Transformers - name: "transformers" - description: "Hugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tuning on NLP, vision, audio, and multimodal tasks.…
### Scientific Schematics - name: "scientific-schematics" - description: "Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality re…
- Skillseaborn
### Seaborn - name: "seaborn" - description: "Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for…
### Scientific Critical Thinking - name: "scientific-critical-thinking" - description: "Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders…
### Scientific Visualization - name: "scientific-visualization" - description: "Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotati…
- Skillscientific-slides
### Scientific Slides - name: "scientific-slides" - description: "Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presenta…
- Skilltimesfm-forecasting
### Timesfm Forecasting - name: "timesfm-forecasting" - description: "Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather…
- Skillscikit-survival
### Scikit Survival - name: "scikit-survival" - description: "Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival da…
- Skilltorchdrug
### Torchdrug - name: "torchdrug" - description: "PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reas…
- Skillstable-baselines3
### Stable Baselines3 - name: "stable-baselines3" - description: "Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick pro…
- Skillshap
### Shap - name: "shap" - description: "Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importan…
- Skillscvelo
### Scvelo - name: "scvelo" - description: "RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver…
- Skillstatistical-analysis
### Statistical Analysis - name: "statistical-analysis" - description: "Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking…
- Skilltorch-geometric
### Torch Geometric - name: "torch-geometric" - description: "PyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbo…
- Skillscikit-learn
### Scikit Learn - name: "scikit-learn" - description: "Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensiona…
- Skillpdf
### Pdf - name: "pdf" - description: "Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitti…
- Skillpymatgen
### Pymatgen - name: "pymatgen" - description: "Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational mater…
- Skilloptimize-for-gpu
### Optimize For Gpu - name: "optimize-for-gpu" - description: "GPU-accelerate Python code using CuPy, Numba CUDA, Warp, cuDF, cuML, cuGraph, KvikIO, cuCIM, cuxfilter, cuVS, cuSpatial, and RAFT. Use whenever the user me…
- Skillpymc
### Pymc - name: "pymc" - description: "Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference."
- Skillpaper-lookup
### Paper Lookup - name: "paper-lookup" - description: "Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles. Covers PubMed, PMC (full text), bioRxiv, medRxiv, arXiv, O…
- Skillpaperzilla
### Paperzilla - name: "paperzilla" - description: "Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical paper detail…
### Protocolsio Integration - name: "protocolsio-integration" - description: "Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, crea…
- Skillphylogenetics
### Phylogenetics - name: "phylogenetics" - description: "Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree.…
- Skillpathway-enrichment
### Pathway Enrichment - name: "pathway-enrichment" - description: "Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (d…
- Skillpacsomatic
### Pacsomatic - name: "pacsomatic" - description: "Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-…
- Skillpolars-bio
### Polars Bio - name: "polars-bio" - description: "High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/…
- Skillpolars
### Polars - name: "polars" - description: "Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow bac…
- Skillscholar-evaluation
### Scholar Evaluation - name: "scholar-evaluation" - description: "Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including pr…
- Skillpathml
### Pathml - name: "pathml" - description: "Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph const…
- Skillprimekg
### Primekg - name: "primekg" - description: "Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more."
### Opentrons Integration - name: "opentrons-integration" - description: "Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Prot…
- Skillqutip
### Qutip - name: "qutip" - description: "Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics…
- Skillscanpy
### Scanpy - name: "scanpy" - description: "Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. B…