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pydantic
Data validation and settings management using Python type annotations with Pydantic v2
pyopenms
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.
pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
python-best-practices
Provides Python patterns for type-first development with dataclasses, discriminated unions, NewType, and Protocol. Must use when reading or writing Python files.
python-database-patterns
SQLAlchemy and database patterns for Python. Triggers on: sqlalchemy, database, orm, migration, alembic, async database, connection pool, repository pattern, unit of work.
python-fastapi
Python FastAPI development with uv package manager, modular project structure, SQLAlchemy ORM, and production-ready patterns.
query-builder
Interactive database query builder for generating optimized SQL and NoSQL queries.
query-optimizer
Analyze and optimize SQL queries for better performance and efficiency.
querying-logseq-data
Expert in building Datalog queries for Logseq DB graphs. Auto-invokes when users need help writing Logseq queries, understanding Datalog syntax, optimizing query performance, or working with the Datascript query engine. Covers advanced query patterns, pull syntax, aggregations, and DB-specific query techniques.
qutip
Quantum mechanics simulations and analysis using QuTiP (Quantum Toolbox in Python). Use when working with quantum systems including: (1) quantum states (kets, bras, density matrices), (2) quantum operators and gates, (3) time evolution and dynamics (Schrödinger, master equations, Monte Carlo), (4) open quantum systems with dissipation, (5) quantum measurements and entanglement, (6) visualization (