eturkes/claude-scientific-skills

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hypogenic Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explo…

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imaging-data-commons Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-…

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iso-13485-certification Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Syste…

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labarchive-integration Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate wi…

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markitdown Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transc…

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medchem Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert c…

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modal Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or se…

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molfeat Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert S…

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neuropixels-analysis Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB d…

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parallel-web All-in-one web toolkit powered by parallel-cli, with a strong emphasis on academic and scientific sources. Use this s…

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pathml Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence…

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pptx Use this skill any time a .pptx file is involved in any way — as input, output, or both. This includes: creating slid…

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pptx-posters Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explici…

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primekg Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, disease…

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pydeseq2 Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR co…

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pydicom Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when rea…

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pylabrobot Vendor-agnostic lab automation framework.

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pymoo Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZD…

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pyopenms Complete mass spectrometry analysis platform.

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pytdc Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molec…

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rdkit Cheminformatics toolkit for fine-grained molecular control.

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rowan Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa a…

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scanpy Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE),…

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scientific-brainstorming Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary co…

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scvelo RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajec…

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seaborn Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and cat…

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sympy Use when you need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or co…

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tiledbvcf Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample …

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transformers Hugging Face Transformers for loading Hub models, running pipeline inference, text generation, and Trainer fine-tunin…

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vaex Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM.

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venue-templates Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publica…

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xlsx Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm) where the workbook file is the primary deliverabl…

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zarr-python Chunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, parallel I/O, S3/GCS via fsspec, NumPy/Dask/…

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adaptyv How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieva…

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astropy Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coor…

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benchling-integration Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling App…

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biopython Comprehensive molecular biology toolkit.

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bioservices Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL,…

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cirq Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or…

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clinical-decision-support Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, in…

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deepchem Molecular ML with diverse featurizers and pre-built datasets.

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deeptools NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), …

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depmap Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivi…

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dhdna-profiler Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how…

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diffdock DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus S…

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dnanexus-integration DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, …

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etetoolkit Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NC…

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geniml This skill should be used when working with genomic interval data (BED files) for machine learning tasks.

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geopandas Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when …

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ginkgo-cloud-lab Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab…

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