claude-scientific-skills
github.com/K-Dense-AI/claude-scientific-skills
Skill | Added | Review |
|---|---|---|
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. | 90 1.51x Agent success vs baseline Impact 82% 1.51xAverage score across 3 eval scenarios Securityby  Passed No known issues Reviewed: Version: cbcae7b | |
rowan Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue docking, protein-ligand cofolding, MSA generation, molecular dynamics, permeability, descriptor workflows, and related small-molecule or protein modeling tasks. Ideal for programmatic batch screening, multi-step chemistry pipelines, and workflows that would otherwise require maintaining local HPC/GPU infrastructure. | 63 Impact — No eval scenarios have been run Securityby Risky Do not use without reviewing Reviewed: Version: cbcae7b | |
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. | 47 Impact — No eval scenarios have been run Securityby Passed No known issues Reviewed: Version: cbcae7b | |
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 around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms. | 81 1.38x Agent success vs baseline Impact 93% 1.38xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
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. | 85 1.40x Agent success vs baseline Impact 90% 1.40xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
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. | 87 1.39x Agent success vs baseline Impact 99% 1.39xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
pytdc Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction. | 72 1.16x Agent success vs baseline Impact 91% 1.16xAverage score across 3 eval scenarios Securityby Advisory Suggest reviewing before use Reviewed: Version: cbcae7b | |
markitdown Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more. | 74 3.40x Agent success vs baseline Impact 85% 3.40xAverage score across 3 eval scenarios Securityby Advisory Suggest reviewing before use Reviewed: Version: cbcae7b | |
matplotlib Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization. | 78 1.06x Agent success vs baseline Impact 94% 1.06xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
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 data processing. For simple spectral comparison and metabolite ID use matchms. | 63 Impact — No eval scenarios have been run Securityby Passed No known issues Reviewed: Version: cbcae7b | |
pymoo Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems. | 80 2.06x Agent success vs baseline Impact 93% 2.06xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
pymc Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference. | 85 1.49x Agent success vs baseline Impact 88% 1.49xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
pymatgen Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science. | 87 1.13x Agent success vs baseline Impact 95% 1.13xAverage score across 3 eval scenarios Securityby Advisory Suggest reviewing before use Reviewed: Version: cbcae7b | |
pylabrobot Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler. | 75 1.20x Agent success vs baseline Impact 87% 1.20xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
pydeseq2 Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis. | 56 Impact — No eval scenarios have been run Securityby Passed No known issues Reviewed: Version: cbcae7b | |
pufferlib High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups over standard implementations. For quick prototyping or standard algorithm implementations with extensive documentation, use stable-baselines3 instead. | 91 1.50x Agent success vs baseline Impact 87% 1.50xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
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. | 82 1.56x Agent success vs baseline Impact 97% 1.56xAverage score across 3 eval scenarios Securityby Risky Do not use without reviewing Reviewed: Version: cbcae7b | |
pptx-posters Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration. | 80 1.48x Agent success vs baseline Impact 83% 1.48xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
polars 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 backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex. | 87 1.01x Agent success vs baseline Impact 86% 1.01xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
pennylane Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch/JAX/TensorFlow. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip. | 88 1.07x Agent success vs baseline Impact 89% 1.07xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
peer-review Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation. | 76 1.10x Agent success vs baseline Impact 93% 1.10xAverage score across 3 eval scenarios Securityby Advisory Suggest reviewing before use Reviewed: Version: cbcae7b | |
pathml Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler. | 77 2.74x Agent success vs baseline Impact 96% 2.74xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
opentrons-integration Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot. | 73 1.11x Agent success vs baseline Impact 85% 1.11xAverage score across 3 eval scenarios Securityby Passed No known issues Reviewed: Version: cbcae7b | |
omero-integration Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows. | 72 1.49x Agent success vs baseline Impact 88% 1.49xAverage score across 3 eval scenarios Securityby Advisory Suggest reviewing before use Reviewed: Version: cbcae7b | |
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. | 72 Impact — No eval scenarios have been run Securityby Advisory Suggest reviewing before use Reviewed: Version: cbcae7b |