Dados e Análise

End-to-end gene regulatory network inference pipeline from processed single-cell data to regulon discovery and perturbation simulation. Supports RNA-only (pySCENIC) and multiome (SCENIC+) paths. Use when building gene regulatory networks from single-cell transcriptomic or multiome data.

End-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.

Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous s

Use when working with Next.js 15 features, App Router, Server Components, Server Actions, or data fetching patterns. Ensures correct usage of Server vs Client Components and modern Next.js patterns.

ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.

Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data. Use when investigating outbreak transmission chains or identifying superspreaders.

Python 3.14 enterprise standards — modern typing (PEP 649), immutable dataclasses, Protocol-based DI, asyncio discipline, pytest 9, psycopg + .sql files via importlib.resources. Use when writing, reviewing, or scaffolding Python code.

Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib and modern alternatives. Use when creating tree figures, customizing colors and labels, exporting to image formats, or choosing between Bio.Phylo, ggtree, ETE4, and iTOL for publication.

Manage database schema changes with version control. Use when modifying DB schema, adding tables/columns, or setting up new projects. Covers Prisma, Drizzle, and migration best practices.

NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.

Master SurrealDB 2.3.x with Python for multi-model database operations including CRUD, graph relationships, vector search, and real-time queries. Use when working with SurrealDB databases, implementing graph traversal, semantic search with embeddings, or building RAG applications.

Download sequencing data from NCBI SRA using the SRA toolkit. Use when downloading FASTQ files from SRA accessions, prefetching large datasets, or validating SRA downloads.