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90 lines
4.6 KiB
Markdown
90 lines
4.6 KiB
Markdown
# Claude Scientific Skills
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A comprehensive collection of ready-to-use scientific skills for Claude, curated by the K-Dense team. These skills enable Claude to work with specialized scientific libraries and databases across bioinformatics, cheminformatics, machine learning, materials science, and data analysis.
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## Available Skills
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### Scientific Databases
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- **PubChem** - Access chemical compound data from the world's largest free chemical database (110M+ compounds, 270M+ bioactivities)
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### Scientific Packages
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**Bioinformatics & Genomics:**
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- **AnnData** - Annotated data matrices for single-cell genomics and h5ad files
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- **Arboreto** - Gene regulatory network inference using GRNBoost2 and GENIE3
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- **BioPython** - Sequence manipulation, NCBI database access, BLAST searches, alignments, and phylogenetics
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- **BioServices** - Programmatic access to 40+ biological web services (KEGG, UniProt, ChEBI, ChEMBL)
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- **Cellxgene Census** - Query and analyze large-scale single-cell RNA-seq data
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- **gget** - Efficient genomic database queries (Ensembl, UniProt, NCBI, PDB, COSMIC)
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- **PyDESeq2** - Differential gene expression analysis for bulk RNA-seq data
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- **Scanpy** - Single-cell RNA-seq analysis with clustering, marker genes, and UMAP/t-SNE visualization
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**Cheminformatics & Drug Discovery:**
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- **Datamol** - Molecular manipulation and featurization with enhanced RDKit workflows
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- **DeepChem** - Molecular machine learning, graph neural networks, and MoleculeNet benchmarks
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- **DiffDock** - Diffusion-based molecular docking for protein-ligand binding prediction
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- **MedChem** - Medicinal chemistry analysis, ADMET prediction, and drug-likeness assessment
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- **Molfeat** - 100+ molecular featurizers including fingerprints, descriptors, and pretrained models
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- **PyTDC** - Therapeutics Data Commons for drug discovery datasets and benchmarks
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- **RDKit** - Cheminformatics toolkit for molecular I/O, descriptors, fingerprints, and SMARTS
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**Machine Learning & Deep Learning:**
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- **PyMC** - Bayesian statistical modeling and probabilistic programming
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- **PyMOO** - Multi-objective optimization with evolutionary algorithms
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- **PyTorch Lightning** - Structured PyTorch training with automatic optimization
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- **scikit-learn** - Machine learning algorithms, preprocessing, and model selection
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- **Torch Geometric** - Graph Neural Networks for molecular and geometric data
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- **Transformers** - Hugging Face transformers for NLU, image classification, and generation
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- **UMAP-learn** - Dimensionality reduction and manifold learning
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**Materials Science & Chemistry:**
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- **Astropy** - Astronomy and astrophysics (coordinates, cosmology, FITS files)
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- **COBRApy** - Constraint-based metabolic modeling and flux balance analysis
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- **Pymatgen** - Materials structure analysis, phase diagrams, and electronic structure
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**Data Analysis & Visualization:**
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- **Matplotlib** - Publication-quality plotting and visualization
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- **Polars** - High-performance DataFrame operations with lazy evaluation
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- **Seaborn** - Statistical data visualization
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- **ReportLab** - Programmatic PDF generation for reports and documents
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**Phylogenetics & Trees:**
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- **ETE Toolkit** - Phylogenetic tree manipulation, visualization, and analysis
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**Genomics Tools:**
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- **deepTools** - NGS data analysis (ChIP-seq, RNA-seq, ATAC-seq) with BAM/bigWig files
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- **FlowIO** - Flow Cytometry Standard (FCS) file reading and manipulation
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- **scikit-bio** - Bioinformatics sequence analysis and diversity metrics
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- **Zarr** - Chunked, compressed N-dimensional array storage
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**Multi-omics & Integration:**
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- **BioMNI** - Multi-omics data integration with LLM-powered analysis
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## Try in Claude Code, Claude.ai, and the API
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### Claude Code
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You can register this repository as a Claude Code Plugin marketplace by running the following command in Claude Code:
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```
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/plugin marketplace add K-Dense-AI/claude-scientific-skills
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```
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Then, to install a specific set of skills:
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1. Select Browse and install plugins
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2. Select claude-scientific-skills
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3. Select scientific-databases or scientific-packages
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4. Select Install now
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After installing the plugin, you can use the skill by just mentioning it. Additionally, in most case, Claude Code will figure out what to use based on the task.
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### Claude.ai
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These example skills are all already available to paid plans in Claude.ai.
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To use any skill from this repository or upload custom skills, follow the instructions in [Using skills in Claude](https://docs.anthropic.com/claude/skills).
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### Claude API
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You can use Anthropic's pre-built skills, and upload custom skills, via the Claude API. See the [Skills API Quickstart](https://docs.anthropic.com/claude/skills-api-quickstart) for more.
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