eturkes/claude-scientific-skills

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glycoengineering Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosyla…

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gtars High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic re…

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lamindb Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers se…

eturkes/claude-scientific-skills

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latchbio-integration Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serve…

eturkes/claude-scientific-skills

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market-research-reports Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartn…

eturkes/claude-scientific-skills

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matchms Spectral similarity and compound identification for metabolomics.

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networkx Create, analyze, and visualize complex networks and graphs in Python with NetworkX. Use when working with network/gra…

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opentrons-integration Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardw…

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paperzilla Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for rece…

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pdf Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables…

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pennylane Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradien…

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polars High-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data man…

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polars-bio High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merg…

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protocolsio-integration Integration with protocols.io API for managing scientific protocols.

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pufferlib High-performance reinforcement learning framework optimized for speed and scale.

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pyhealth Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, …

eturkes/claude-scientific-skills

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pymatgen Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project i…

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pymc Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, post…

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pysam Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, c…

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pytorch-lightning Deep learning framework (PyTorch Lightning / lightning package).

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qiskit IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production …

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qutip Quantum physics simulation library for open quantum systems.

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scholar-evaluation Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across resear…

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scikit-bio Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), …

eturkes/claude-scientific-skills

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scikit-learn Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression),…

eturkes/claude-scientific-skills

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scikit-survival Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skil…

eturkes/claude-scientific-skills

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shap Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining …

eturkes/claude-scientific-skills

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simpy Process-based discrete-event simulation framework in Python.

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torchdrug PyTorch-native graph neural networks for molecules and proteins.

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treatment-plans Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties.

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umap-learn Use UMAP-learn for nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi…

eturkes/claude-scientific-skills

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usfiscaldata Query the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (…

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what-if-oracle Run structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card, con…

eturkes/claude-scientific-skills

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hugging-science Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate,…

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autoskill Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-…

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paper-2-web This skill should be used when converting academic papers into promotional and presentation formats including interac…

eturkes/claude-scientific-skills

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exa-search Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search …

eturkes/claude-scientific-skills

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denario Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publi…

eturkes/claude-scientific-skills

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plotly Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashbo…

eturkes/claude-scientific-skills

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research-lookup Look up current research information using parallel-cli search (primary, fast web search), the Parallel Chat API (dee…

eturkes/claude-scientific-skills

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bids Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical…

eturkes/claude-scientific-skills

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pacsomatic Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user …

eturkes/claude-scientific-skills

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bulk-rnaseq End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), ali…

eturkes/claude-scientific-skills

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liteparse Local document and PDF parsing with spatial text and bounding boxes.

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nextflow Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextfl…

eturkes/claude-scientific-skills

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pathway-enrichment Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whene…

eturkes/claude-scientific-skills

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arbor Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objecti…

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experimental-design Design experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out tr…

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pi-agent Build with and use Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/setti…

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statistical-power Sample-size and statistical power calculations for planning studies. Use whenever someone asks "how many subjects/sam…

eturkes/claude-scientific-skills

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