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Build applications powered by GitHub Copilot using the Copilot SDK. Use when creating programmatic integrations with Copilot across Node.js/TypeScript, Python, Go, or .NET. Covers session management, custom tools, streaming, hooks, MCP servers, BYOK providers, session persistence, and custom agents. Requires GitHub Copilot CLI installed and a GitHub Copilot subscription (unless using BYOK).

CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). Bin coverage in target/antitarget regions, normalize vs reference, segment with CBS/HMM, call amps/dels, scatter/diagram plots, purity/ploidy, VCF/SEG export. CLI plus Python API (cnvlib). Use GATK CNV for deep WGS with population controls; use CNVkit for targeted/exome where antitarget bins matter.

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

Use esta skill sempre que Claude precisar escrever, sugerir ou executar comandos shell, scripts ou instruções de terminal, especialmente em contextos de codificação de IA. Ela suporta scripts bash/shell, comandos SSH, operações Docker, comandos Git, ambientes virtuais Python, PowerShell, Windows CMD e tarefas CLI multiplataforma.

Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series, rigorous inference with coefficient tables. For guided statistical test selection with APA reporting use statistical-analysis.

Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups, midpoint, or MAD methods, pruning taxa, collapsing clades, ladderizing branches, or extracting subtrees. Includes rooting method decision guidance.

Core Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms (ICRS/Galactic/AltAz/FK5), FITS I/O, tables (FITS/HDF5/VOTable/CSV), cosmology (Planck18, distance/age), precise time (UTC/TAI/TT/TDB, Julian, barycentric), WCS pixel-world mapping, model fitting. For general tables use pandas/polars; for radio interferometry use CASA.

SDK do Azure Cosmos DB para Python (API NoSQL). Use para operações CRUD de documentos, consultas, contêineres e dados distribuídos globalmente.

Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. Automates Fiji headlessly from Python. Use scikit-image for pure Python without Fiji plugins; napari for visualization.

Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.