Explorar skills

Enforces TDD discipline with RED-GREEN-REFACTOR cycle. Use when writing new features, fixing bugs, or refactoring code. Ensures tests genuinely verify behavior.

Execute coding tasks with a strict delivery workflow: build a full plan, implement one step at a time, run tests continuously, and commit by default after each step (`per_step`). Support explicit commit policy overrides (`final_only`, `milestone`) and optional BDD (Given/When/Then) when users ask for behavior-driven delivery or requirements are unclear.

Discover and deliver repository optimization work end to end: identify performance/reliability/maintainability/security/dx/cost optimization points, prioritize by impact-effort-risk, then execute fixes step by step with continuous testing and explicit commit policy (`final_only`, `per_step`, `milestone`). Default to `per_step` for implementation work so each feature is tested then committed before

Complete testing strategy covering TDD workflow, test pyramid, unit/integration/E2E/property testing, framework best practices (Jest, Vitest, pytest), mock strategies, and CI integration. Use when writing tests, reviewing test quality, or establishing testing standards.

Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.

Consulte a API REST STRING para interações proteína-proteína (PPIs) em 59M proteínas, 20B interações e mais de 5000 espécies, permitindo a recuperação de redes, enriquecimento GO/KEGG, localização de parceiros, teste de significância de PPIs, visualização de redes e análise de homologia. Para interações químicas, use chembl-database-bioactivity; para vias, use kegg-database.

Guided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. Pick tests, verify assumptions, or format results for publication. Covers frequentist (t-test, ANOVA, chi-square, regression, correlation, survival, count, reliability) and Bayesian. Use statsmodels or pymc-bayesian-modeling to fit.

Graph and network analysis toolkit. Four graph types (directed, undirected, multi-edge), centrality, shortest paths, community detection, generators, I/O (GraphML, GML, edge list), matplotlib viz. For large graphs (100K+ nodes) use igraph or graph-tool; for GNNs use PyG.

Filter degenerate, uninformative inputs before statistical tests: single-sequence alignments, empty files, constant features, zero-variance inputs, all-NaN columns. See nan-safe-correlation for NaN-aware correlation; statistical-analysis for test guidance.

MaxQuant + Perseus proteomics pipeline: run MaxQuant for LFQ and SILAC; parse proteinGroups.txt in Python; filter contaminants/decoys; log2 + median-normalize; impute MNAR; t-test with FDR; volcano plot; GO/pathway enrichment. Use Proteome Discoverer for Thermo-native processing; FragPipe/MSFragger for GPU-accelerated DB search.

Structured hypothesis formulation: turn observations into testable hypotheses with predictions, propose mechanisms, design experiments. Follows the scientific method. Use scientific-brainstorming for open ideation; hypogenic for automated LLM hypothesis testing on datasets.

Per-feature NaN-safe Spearman/Pearson correlation across many features (genes, proteins, variants) with missing values. Covers why bulk matrix shortcuts fail, correct pairwise deletion, degenerate input filtering, and large-dataset performance. Use statistical-analysis for test choice; shap-model-explainability for interpretability.