deepspeed
Expert guidance for distributed training with DeepSpeed - ZeRO optimization stages, pipeline parallelism, FP16/BF16/FP8, 1-bit Adam, sparse attention
dependency-auditor
Check dependencies for known vulnerabilities using npm audit, pip-audit, etc. Use when package.json or requirements.txt changes, or before deployments. Alerts on vulnerable dependencies. Triggers on dependency file changes, deployment prep, security mentions.
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
denario
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
deepchem
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.
diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
e2e-testing-patterns
Master end-to-end testing with Playwright and Cypress to build reliable test suites that catch bugs, improve confidence, and enable fast deployment. Use when implementing E2E tests, debugging flaky tests, or establishing testing standards.
docx
Comprehensive document creation, editing, and analysis with support for tracked changes, comments, formatting preservation, and text extraction. When Claude needs to work with professional documents (.docx files) for: (1) Creating new documents, (2) Modifying or editing content, (3) Working with tracked changes, (4) Adding comments, or any other document tasks
dspy
Build complex AI systems with declarative programming, optimize prompts automatically, create modular RAG systems and agents with DSPy - Stanford NLP's framework for systematic LM programming
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
elevenlabs-agents
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etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
domain-name-brainstormer
Generates creative domain name ideas for your project and checks availability across multiple TLDs (.com, .io, .dev, .ai, etc.). Saves hours of brainstorming and manual checking.
dependency-upgrade
Manage major dependency version upgrades with compatibility analysis, staged rollout, and comprehensive testing. Use when upgrading framework versions, updating major dependencies, or managing breaking changes in libraries.
error-handling-patterns
Master error handling patterns across languages including exceptions, Result types, error propagation, and graceful degradation to build resilient applications. Use when implementing error handling, designing APIs, or improving application reliability.
ena-database
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
deployment-pipeline-design
Design multi-stage CI/CD pipelines with approval gates, security checks, and deployment orchestration. Use when architecting deployment workflows, setting up continuous delivery, or implementing GitOps practices.
flowio
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
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