mkurman/zorai - 第 12 页

pymc

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

原文语言：英语

pyopenms

Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS…

原文语言：英语

pysam

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

原文语言：英语

pytdc

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

原文语言：英语

pytorch-lightning

Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural…

原文语言：英语

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…

原文语言：英语

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…

原文语言：英语

rdkit

Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper…

原文语言：英语

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…

原文语言：英语

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.

原文语言：英语

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…

原文语言：英语

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…

原文语言：英语

scientific-visualization

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…

原文语言：英语

scikit-bio

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

原文语言：英语

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…

原文语言：英语

scikit-survival

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…

原文语言：英语

scvi-tools

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,…

原文语言：英语

seaborn

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…

原文语言：英语

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),…

原文语言：英语

simpleitk

Simplified interface to the Insight Toolkit (ITK) for medical image processing. Segmentation, registration, filtering, resampling, morphological operations. Supports DICOM, NIfTI, NRRD, dozens of formats.

原文语言：英语

stable-baselines3

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…

原文语言：英语

statsmodels

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…

原文语言：英语

sympy

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…

原文语言：英语

tensorrt

NVIDIA TensorRT — deep learning inference optimizer. FP16/INT8/INT4 quantization, kernel auto-tuning, layer fusion, and dynamic shapes. Max throughput on NVIDIA GPUs for production inference.

原文语言：英语

tiledbvcf

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.

原文语言：英语

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…

原文语言：英语

total-segmentator

Tool for robust segmentation of 104+ anatomical structures in CT images. Uses nnUNet-based models for whole-body, organ, and bone segmentation. One-line CLI for comprehensive body-part segmentation.

原文语言：英语

transformers

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…

原文语言：英语

treatment-plans

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.…

原文语言：英语

umap-learn

UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.

原文语言：英语

vaex

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…

原文语言：英语

xlsx

Use this skill any time a spreadsheet file is the primary input or output. This means any task where the user wants to: open, read, edit, or fix an existing .xlsx, .xlsm, .csv, or .tsv file (e.g., adding columns, computing formulas, formatting, charting,…

原文语言：英语

zarr-python

Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.

原文语言：英语

synthlabs-curation

Use when SynthLabs dataset curation should run as repeatable background HTTP jobs instead of manual UI work.

原文语言：英语

synthlabs-generation

Use when you need to drive SynthLabs generation through backend routes instead of the UI.

原文语言：英语

synthlabs-setup

Use when you need to locate, start, and verify a local SynthLabs backend before API-dependent work.

原文语言：英语

synthlabs-ui-operator

Use when SynthLabs work must be driven through the visual app for verifier review, data preview, settings changes, DEEP mode, or other browser-led workflows.

原文语言：英语

approval-checkpoint-long-task

Canonical long-task pack for daemon-managed work with deliberate approval checkpoints, status summaries, rollback notes, and mobile-safe governance-aware updates.

原文语言：英语

daily-brief

Canonical daily brief pack for day-start summaries across tasks, routines, approvals, notices, and optional Gmail/Calendar connectors.

原文语言：英语

inbox-calendar-triage

Canonical inbox and calendar triage pack for agenda prep, urgent unread mail, follow-ups, and draft-only response suggestions.

原文语言：英语