「express」の検索結果

Fires after fixing any non-trivial bug or regression. Asks: could the graph have caught this as a guarantee? Pairs with reflection-in-and-on-action — picks up after "earliest catchable signal" and asks the next question: was that signal expressible in graph? Triggers: (1) after any non-trivial bug fix is verified working, (2) after a regression report (something used to work, broke), (3) during step 6 (knowledge extraction) of the workflow, (4) when reflection-on-action surfaces a "would have been catchable" signal. Outcome is a triage decision (graph-reachable? rule expressible? rule sound?) and either a draft Linear issue + guarantee proposal, or a recorded "graph capability gap" note. Never auto-creates guarantees.

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AI-DLC v3（AI-Driven Development Lifecycle）のオーケストレーター。 define / develop / release / reflect の 4 フェーズコマンドと status / doctor の 補助コマンド、連続実行ラッパ express、旧名エイリアス（inception / construction / operations / retrospective）を統一的にルーティングする。 define / develop（normal / risky 含む）/ release / reflect の各フェーズフローと status / doctor の補助コマンドを実装済み（doctor は shallow scope）。

Build and validate Azure infrastructure in a lab or sandbox using Azure CLI and official Microsoft docs. Use when creating verification environments, provisioning hub-and-spoke VNets, VPN Gateway or ExpressRoute-adjacent validation labs, checking subscription/tenant access, debugging Azure deployment constraints, comparing before/after route behavior, or cleaning up lab resources. Triggers on 'Azure 検証', '検証環境', 'PoC', 'sandbox', 'lab', 'Azure CLI で構築', 'VPN Gateway', 'VNet peering', 'BGP', 'route validation', 'summarizedGatewayPrefixes', 'デプロイして検証', 'インフラ検証'.

"Apply spiral of silence theory (Noelle-Neumann) to analyze how perceived opinion climate suppresses minority expression. Use this skill when the user needs to understand why certain viewpoints disappear from public discourse, evaluate the role of fear of isolation in opinion expression, or assess opinion climate dynamics — even if they say 'why are people afraid to speak up', 'silent majority', or 'social pressure on opinions'.".

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Express.js routes, middleware, error handling, request/response patterns

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Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the user wants to find GEO accessions for ENCODE experiments, search GEO for complementary datasets, download GEO metadata or series matrices, cross-reference ENCODE and GEO data, find supplementary files from GEO, or link GEO series to ENCODE experiments for provenance tracking. Also use when the user mentions GEO, GSE, GSM, GPL, GDS, series matrix, SOFT format, or needs to find expression data in GEO that complements their ENCODE analysis.

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Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need cell-type-specific expression context for ENCODE regulatory data, want to deconvolve bulk ENCODE signals, or validate regulatory elements at single-cell resolution. Trigger on: CellxGene, single-cell atlas, cell type expression, Census, cell type specificity, single-cell context, scRNA-seq atlas.

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Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification, TPM, FPKM, RNA processing, run RNA-seq.

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Express.js API guidance — routing, middleware architecture, error handling, security hardening, and production setup.

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Use this skill when configuring or troubleshooting FSC Referral Management: setting up referral types via ReferralRecordTypeMapping custom metadata, routing referrals through Lead Assignment Rules keyed on the Expressed Interest picklist, tracking Referrer Score, and partner referral visibility in Experience Cloud. Trigger keywords: referral routing, FSC referral types, ReferralRecordTypeMapping, Expressed Interest picklist, partner referral Contact, Referrer Score Experience Cloud. NOT for clinical referrals in Health Cloud — use admin/referral-management-health. NOT for standard Lead capture and conversion outside FSC — use admin/lead-management-and-conversion.

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Opinionated house conventions for NestJS backends — module boundaries and layering, provider wiring and injection scopes, guards/interceptors/pipes/filters, DTOs and validation, domain exceptions, config, and the Nest 11 / Express 5 behaviour that compiles cleanly and fails at runtime. Use whenever the code is NestJS (`@nestjs/*` in package.json, or `@Module`/`@Injectable`/`@Controller`/`@Cron` in the file), including when the question sounds like plain TypeScript, an OOP refactor, a code review, or an ops problem — the Nest-specific answer differs from the generic one. Typical asks: scaffolding a module, adding a controller, provider, or endpoint, wiring an enhancer, a boot-time DI or circular-import failure, a response leaking entity fields despite `@Exclude()`, a cron job firing on every replica, upgrading NestJS, or reviewing a Nest diff. Not for plain Express or Fastify, Angular, frontend, SQL, or CI.

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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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Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-bias-aware differential via its bam_ip/bam_input control + bam_treated_ip/bam_treated_input treatment arms), QNB beta-binomial, MeTDiff HMM, and RADAR, plus the paired-symmetric edgeR/DESeq2-on-peak-counts route when batch/lot covariates need fixed-effect handling that exomePeak2's API does not accept. Covers paired vs unpaired vs interaction designs, batch confounding and per-lot meta-analysis, the stoichiometry-vs-expression-vs-IP-efficiency confound, and effect-size filtering against under-powered N=2 designs. Use when comparing m6A across two or more conditions, choosing between exomePeak2/QNB/RADAR/MeTDiff for a design, handling batch confounding when exomePeak2's API is too rigid, distinguishing real hyper/hypo-methylation from expression shifts, applying effect-size thresholds, or planning orthogonal stoichiometry validation (GLORI/SAC-seq/m6Anet mod_ratio).

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Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE DESeq), LRT reduced-model rules, the interaction-term resultsNames trap, continuous-covariate scaling and splines, repeated measures via duplicateCorrelation or dream, high-cardinality categorical pseudo-singular designs, sample swap detection via XIST/RPS4Y1 expression and somalier/NGSCheckMate genotypes, SABV (sex-as-biological-variable) mandate, Simpson's-paradox collapsing of technical replicates, and the `~ 0 + group` parameterization for clean contrasts. Use when building a design matrix, troubleshooting reversed fold-change direction, encoding paired or repeated-measures designs, detecting sample swaps, deciding sex-as-covariate, or aggregating technical replicates.

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Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering, and ComplexHeatmap/pheatmap/seaborn rendering. Covers the ward.D vs ward.D2 trap, the row-vs-column scaling decision, multi-track annotations, oncoPrint, and raster rendering for large matrices. Use when visualizing expression patterns across samples or identifying co-regulated clusters.

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Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions. Covers EnhancedVolcano, ggplot2, matplotlib, and the apeglm/ashr/normal shrinkage decision. Use when visualizing differential-expression results (RNA-seq, ChIP-seq, ATAC-seq, proteomics) or any per-feature effect-size + p-value table.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier handling, VST/rlog transforms, and design formulas including paired, batch, and interaction terms. Use when running bulk DE, choosing DESeq2 over edgeR or limma-voom, building a paired or interaction design, applying LFC shrinkage for ranking or GSEA, choosing Wald vs LRT, troubleshooting padj=NA, picking VST vs rlog, importing salmon/kallisto via tximport, or analyzing prokaryotic RNA-seq.

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Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.

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Add strategic color to features that are too monochromatic or lack visual interest, making interfaces more engaging and expressive. Use when the user mentions the design looking gray, dull, lacking warmth, needing more color, or wanting a more vibrant or expressive palette.

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Use for deep Node.js / Express project analysis: boot flow, middleware order, async behavior, data layer, auth/security, and Node-specific runtime failure patterns.

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Guia completo de desenvolvimento backend para microserviços Node.js/Express/TypeScript. Use ao criar routes, controllers, services, repositories, middleware ou trabalhar com Express APIs, acesso a banco de dados com Prisma, rastreamento de erros com Sentry, validação com Zod, unifiedConfig, injeção de dependências ou padrões assíncronos. Cobre arquitetura em camadas (routes → controllers → services → repositories), padrão BaseController, tratamento de erros, monitoramento de performance, estratégias de testes e migração de padrões legados.

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Add strategic color to features that are too monochromatic or lack visual interest, making interfaces more engaging and expressive. Use when the user mentions the design looking gray, dull, lacking warmth, needing more color, or wanting a more vibrant or expressive palette.

日本語の概要は準備中です。原文の説明を表示しています。