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