Results for “bun”

Work on the dashboard's frontend — the vanilla JS/CSS page with no framework or bundler. Use this whenever a task touches `static/nowplaying.js`, `static/style.css`, the Jinja templates (`templates/nowplaying.html`, `_icons.html`), the accent-color tinting, the karaoke lyrics sync, the now-playing poll, or the empty-state mosaic / recent-plays pile. Covers how the page is wired, how it reads i18n and data from the server, the ESLint gate, and the Android bridge, so changes match the existing patterns.

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Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound, inhomogeneous Ripley's K, cellular-neighborhood discovery, graph-construction (contact vs proximity), and edge effects. Use when testing whether cell types co-locate, choosing a spatial null, building a neighbor graph, discovering tissue niches, or deciding whether a spatial pattern is real or a density/segmentation artifact.

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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.

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Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-analysis).

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Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with `bam_ip` + `bam_input` (control arm) and `bam_treated_ip` + `bam_treated_input` (treatment arm) for integrated GC-bias-aware differential calling (Liu 2022 *NAR Genom Bioinform* 4:lqac046), QNB beta-binomial test (Liu 2017 *BMC Bioinformatics* 18:387), MeTDiff HMM-based differential bundled with MeTPeak, RADAR (Zhang 2019 *Genome Biol* 20:294) with its `filterBins -> diffIP -> reportResult` workflow, and the defensible paired-symmetric case of edgeR / DESeq2 on featureCounts-on-peaks matrices when batch / lot covariates need explicit fixed-effect handling (exomePeak2's top-level API does NOT accept arbitrary covariates). Covers paired vs unpaired vs interaction designs, batch confounding (antibody lot, RNA prep, sequencing run) and the per-lot meta-analysis strategy when exomePeak2 is the primary caller, the stoichiometry-vs-expression-vs-IP-efficiency confound that all MeRIP differential methods inherit, normalisation choice (size factor on IP, on input, on per-sample IP/input ratio), the McIntyre 2020 reproducibility caveat, effect-size filtering as a guardrail against under-powered N=2 designs, and orthogonal-validation routes for absolute stoichiometry (GLORI / SAC-seq / m6Anet `mod_ratio`). Use when comparing m6A levels across two or more conditions, choosing between exomePeak2 / QNB / RADAR / MeTDiff for a given design, handling batch confounding when exomePeak2's API is too rigid, normalising against input properly, distinguishing real hyper- / hypo-methylation from expression-level shifts, applying effect-size thresholds, interpreting volcano plots of differential peaks, or planning a follow-up orthogonal stoichiometry validation.

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Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS. Handles silent-miscounting traps (featureCounts -p v2.0.2 API break, STAR strandedness column choice, salmon NumReads-sum without tximport, RSEM non-integer expected_count, GENCODE _PAR_Y suffix, zero-length-transcript TPM divide-by-zero), and encodes the tximport countsFromAbundance decision tree with the "lengthScaledTPM is not TPM" warning. Use when assembling a gene-by-sample count matrix from aligner or quantifier output, importing salmon/kallisto for DESeq2 vs limma-voom, choosing strandedness column for STAR, debugging zero-count panics, or building tx2gene mapping.

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Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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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-format export.

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Angular performance optimization and best practices guide. Use when writing, reviewing, or refactoring Angular code for optimal performance, bundle size, and rendering efficiency.

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Estimate calcium-normalized Gapon selectivity coefficients from paired exchange and solution chemistry, or initialize depth-explicit EcoSIM Gapon inputs from the closest bundled ecosystem template when paired chemistry is unavailable. Use when deriving or checking EcoSIM GKC4, GKCH, GKCA, GKCM, GKCN, or GKCK values; matching a target ecosystem, climate, vegetation, and management regime to a starting profile; remapping template values to target soil layers; or documenting that template-based values require calibration or tuning.

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Comprehensive end-to-end validation of the Archon Web UI using browser automation and codebase review. Use when: User wants to validate, test, or audit the Archon web interface, find UI/UX bugs, test workflow management, verify parallel agent orchestration, or run comprehensive browser-based E2E tests. Triggers: "validate ui", "test the ui", "e2e test", "browser test", "validate archon", "test archon ui", "ui audit", "ux review", "comprehensive test", "validate everything". Capability: Starts Archon, runs exhaustive browser automation tests via agent-browser CLI, performs codebase review, and produces a detailed bug/UX report. NOT for: Unit tests (use `bun test`), CLI-only validation (use /validation:validate-simple).

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Produce a deterministic, read-only evidence map of the repository for SDD Composy (languages, manifests, commands, modules, boundaries, staleness) and publish the context bundle only on request. Use before a PRD or TechSpec, or when the map is stale — 'mapear o repositório', 'atualizar o contexto do código', 'what does this codebase look like for SDD'. Do NOT use for architecture decisions, code review, or repository exploration without an SDD workspace.

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Initialize or resume the SDD Composy workspace of a repository: preview missing governance and OKF bundle files, apply only approved absent paths, persist the artifact language, and verify. Use when a project needs SDD set up or resumed — 'inicializar o SDD', 'configurar o workspace SDD', 'run init first', or when any SDD skill returned not_initialized. Do NOT use for generic CLAUDE.md or repository setup outside SDD Composy, or for other plugins' init.

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Review or refactor an existing SKILL.md and its bundled resources — a smaller always-loaded core, conditional references, preserved behavior, lean/guided consumer profiles, and an A/B protocol to compare a candidate with the previous version. Use when a skill repeats itself, loads references on every run, triggers too broadly or misses legitimate requests, or needs its efficiency measured across models. Do NOT use for writing a new skill from scratch, refactoring application code, translating a skill verbatim, or performing the target skill's own task.

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Segundo cérebro persistente em Markdown — LLM Wiki no padrão Karpathy mantida como bundle Open Knowledge Format v0.2, com fontes imutáveis em raw/ e conceitos citados em wiki/. Use quando o usuário disser "segundo cérebro", "second brain", "adiciona isso ao meu brain", "salva na minha wiki", "ingere esse artigo/PDF/link", "o que minha wiki diz sobre", "o que meu brain sabe sobre", "consulta meu conhecimento", "lint da wiki", ou pedir para acumular conhecimento de fontes de forma durável. NÃO use para notas do Obsidian (pwdev-obsidian), planejamento de features (pwdev-feat) nem PRDs (pwdev-prd).

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Administração de Ubuntu, Debian e AlmaLinux — systemd, cron, SSH, Fail2Ban, supervisor, disco, memória, rede e processos. Use quando o usuário disser "servidor", "linux", "systemd", "serviço não sobe", "disco cheio", "load alto", "SSH", "cron não roda", "processo travado".

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Quality gates determinísticos para Vue.js, JavaScript e TypeScript. Use quando o usuário pedir "quality gate Vue.js", ESLint, vue-tsc ou Vitest em projeto Vue.js, cobertura, complexidade, bundle, acessibilidade ou baseline para Vue.js.

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React and Next.js performance optimization guidelines from Vercel Engineering. This skill should be used when writing, reviewing, or refactoring React/Next.js code to ensure optimal performance patterns. Triggers on tasks involving React components, Next.js pages, data fetching, bundle optimization, or performance improvements.

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Performance regression detection using the browse daemon. Establishes baselines for page load times, Core Web Vitals, and resource sizes. Compares before/after on every PR. Tracks performance trends over time. Use when: "performance", "benchmark", "page speed", "lighthouse", "web vitals", "bundle size", "load time". (gstack) Voice triggers (speech-to-text aliases): "speed test", "check performance".

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React and Next.js performance optimization guidelines from Vercel Engineering. This skill should be used when writing, reviewing, or refactoring React/Next.js code to ensure optimal performance patterns. Triggers on tasks involving React components, Next.js pages, data fetching, bundle optimization, or performance improvements.

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[BETA] Expert assistance for the Adobe I/O CLI plugin `@adobe/aio-cli-plugin-aem-rde` — the `aio aem rde` / `aio aem:rde` command tree used to deploy, inspect, log-tail, snapshot, and troubleshoot AEM Rapid Development Environments (RDEs). Activate ONLY when the user explicitly references RDE concepts: 'AEM RDE', 'Rapid Development Environment', `aio aem rde`, `aio aem:rde`, `aem-rde`, RDE snapshots, RDE deploy/install, `rde install`, `rde inspect`, `rde status`, `rde history`, `rde reset`, the `@adobe/aio-cli-plugin-aem-rde` package, or Cloud Manager program/environment configuration that is specifically for an RDE environment. Do NOT activate on generic AEMaaCS phrases like 'deploy to AEM Cloud', 'push my bundle', 'tail the publish log', 'cloud sandbox', or unqualified 'dispatcher-config / frontend / env-config deployments' — those belong to Cloud Manager pipelines, not RDE. This skill is in beta. Verify all outputs before applying them to production projects.

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AEM as a Cloud Service Java/OSGi best practices, guardrails, and legacy-to-cloud pattern transformations. Use for Cloud Service–correct bundles, deprecated APIs, schedulers, ResourceChangeListener, replication, Replicator, JCR observation (javax.jcr.observation.EventListener), OSGi Event Admin (org.osgi.service.event.EventHandler), DAM AssetManager, BPA-style fixes, HTL (Sightly) Cloud SDK lint warnings (data-sly-test redundant constant value comparison), or any time you need the detailed pattern reference modules under this skill.

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Use when finishing a feature, fixing a bug, before committing React code, or when the user types `/doctor`, asks to scan, triage, or clean up React diagnostics. Covers lint, accessibility, bundle size, architecture. Includes a regression check and a full local-triage workflow that fetches the canonical playbook.

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Use when finishing a feature, fixing a bug, before committing React code, or when the user asks to scan, triage, or clean up React diagnostics. Covers lint, accessibility, bundle size, architecture, regression checks, and local triage with React Doctor.

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