Dados e Análise

Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation. Use when integrating RNA-seq, proteomics, methylation, or other omics to discover latent factors driving biological variation across modalities.

De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.

Builds automated sports analytics pipelines -- daily data pulls, scheduled prediction generation, model versioning, prediction tracking, and drift alerting. Use when user asks how to automate their model, how to run predictions every morning, how to set up a cron job for sports data, how to track model performance over time, or how to version their model. Do not use for one-time data pulls -- use

BRENDA Enzyme DB SOAP/REST queries: kinetic parameters (Km, Vmax, kcat, Ki), EC classes, substrate specificity, inhibitors, cofactors, organism data. 80K+ enzymes, 7M+ values. Free academic registration. For metabolic modeling use cobrapy-metabolic-modeling; metabolites use hmdb-database.

Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamada-Kawai, hive plots), edge bundling, community-based coloring, and reproducible seeds using NetworkX, PyVis, igraph, and Cytoscape automation. Use when rendering biological networks for static publication, interactive HTML exploration, or Cytoscape-form

Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.

KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a gene list. Supports 4000+ organisms via KEGG online database.

Implement PCI DSS compliance requirements for secure handling of payment card data and payment systems. Use when securing payment processing, achieving PCI compliance, or implementing payment card security measures.

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.

Implement comprehensive server-side validation with allowlists, type checking, input sanitization, and consistent error messages, while using client-side validation for user experience. Use this skill when validating user input, form data, API requests, implementing security checks, preventing injection attacks, checking data types/formats/ranges, or providing validation feedback. Apply when worki

Manages Supabase database schema, migrations, and queries for CookMode V2. Use this when the user needs to create/modify tables, write migrations, update RLS policies, or troubleshoot database issues.

Programmatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints (ESearch, EFetch, ESummary, EPost, ELink), history server for batches, citation matching, systematic review strategies. Use for biomedical literature search or automated pipelines.