「ordering」の検索結果

Detect cell-ordering / enchainement problems in Jupyter notebooks (canonical-order slippage, misplaced or forgotten cells). Arguments: [target] [--severity HIGH|MED|LOW] [--json]

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Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.

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。

Corrects fluorophore spillover (conventional compensation) or spectral overlap (spectral unmixing) and applies variance-stabilizing transforms (logicle/biexponential, arcsinh, log) for flow and mass cytometry. Covers spillover-matrix estimation from single-stain controls, AutoSpill, the spillover spreading matrix and why panel design (not compensation) bounds resolution, compensate-then-transform ordering, and arcsinh cofactor choice (5 for CyTOF, ~150 for fluorescence, per-channel via flowVS). Use when correcting spectral overlap, preparing data for gating/clustering, choosing logicle vs arcsinh, deciding a cofactor, or distinguishing compensation from spectral unmixing.

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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.

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。

Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.

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Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.

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。

Create and scaffold plugin directories for Codex with a required `.codex-plugin/plugin.json`, optional plugin folders/files, and baseline placeholders you can edit before publishing or testing. Use when Codex needs to create a new local plugin, add optional plugin structure, or generate or update repo-root `.agents/plugins/marketplace.json` entries for plugin ordering and availability metadata.

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。

Use when building APIs on Hono (Cloudflare Workers, Bun, Deno, Node), debugging route ordering, wiring middleware, validating with @hono/zod-validator, returning streaming responses, configuring CORS with credentials, handling errors via app.onError, or composing typed RPC clients. Triggers: c.env binding types, c.header + c.redirect interaction, missing await next() bugs, Set-Cookie not attaching to redirect, route-precedence surprises, JWT middleware setup, hono/client typed RPC end-to-end. NOT for Express/Fastify/Koa idioms, tRPC/GraphQL paradigms, or Next.js Route Handlers.

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Use when optimizing Docker builds with BuildKit, designing multi-stage Dockerfiles, leveraging cache mounts, building multi-arch images, choosing distroless vs alpine, or signing images with cosign. Triggers: docker build slow, layer cache not hitting, npm install / pip install reruns, multi-stage final image bloat, glibc vs musl issues, RUN --mount=type=cache, BUILDKIT_INLINE_CACHE, registry cache exporters, qemu emulation for arm64, COPY ordering for cache. NOT for Docker daemon admin, Kubernetes-specific image policies, container security scanning workflows, or Buildpacks (different paradigm).

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Validates DAG structures, performs topological sorting, detects cycles, and resolves dependency conflicts. Uses Kahn's algorithm for optimal execution ordering. Activate on 'resolve dependencies', 'topological sort', 'cycle detection', 'dependency order', 'validate dag'. NOT for building DAGs (use dag-graph-builder) or scheduling execution (use dag-task-scheduler).

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。

Create and scaffold plugin directories for Codex with a required `.codex-plugin/plugin.json`, optional plugin folders/files, valid manifest defaults, and personal-marketplace entries by default. Use when Codex needs to create a new personal plugin, add optional plugin structure, generate or update marketplace entries for plugin ordering and availability metadata, or update an existing local plugin during development with the CLI-driven cachebuster and reinstall flow.

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Use when landing a stack of dependent GitHub PRs (A ← B ← C, where each bases on the one below) onto master, merging a PR whose base is another open PR's branch, or whenever a request mentions "stacked PRs", "PR stack", "dependent PRs", or merging several related PRs in sequence. Requires every same-repository dependency chain to use GitHub's official stacked-PR feature before landing so GitHub owns stack-wide rules, CI, ordering, retargeting, and merge state.

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App Store and Google Play screenshot creation with exact platform specs. Covers iOS/Android dimensions, gallery ordering, device mockups, and preview videos. Use for: app store optimization, ASO, app screenshots, app preview, play store listing. Triggers: app store screenshots, aso, app st...

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Operating manual for Telegram over its MCP connector and roughly 115 tools: how to find a chat by title, the tool inventory grouped by job, resolving chat ids, auto-transcribing voice notes, and the connector gotchas (pinned-first ordering, big-page crashes, reload after reconnect, untrusted fields, always passing an explicit account). Load before any non-trivial Telegram work.

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Use when working with Bandwidth — bandwidth communications platform management for voice calls, SMS/MMS messaging, phone number ordering, and 911 services. Use when managing phone number inventory, analyzing message delivery, monitoring call quality, reviewing usage, or troubleshooting Bandwidth messaging and voice issues.

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API + Python SDK for ordering cell-free protein expression and binding assays. Submit sequences for expression (10–100 µg), measure binding affinity (KD) against targets, track status, and retrieve results programmatically — no wet-lab setup. Built for ML-guided directed evolution and antibody/nanobody optimization. Requires Adaptyv account and API key.

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。

Create and scaffold plugin directories for Codex with a required `.codex-plugin/plugin.json`, optional plugin folders/files, valid manifest defaults, and personal-marketplace entries by default. Use when Codex needs to create a new personal plugin, add optional plugin structure, generate or update marketplace entries for plugin ordering and availability metadata, or update an existing local plugin during development with the CLI-driven cachebuster and reinstall flow.

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。

Guide for MSBuild extensibility: CustomBefore/CustomAfter hooks, wildcard imports with alphabetic ordering, import gating with control properties, NuGet package build extension layout (build/buildTransitive), and the MicrosoftCommonPropsHasBeenImported guard. Only activate in MSBuild/.NET build context. USE FOR: diagnosing and fixing MSBuild import and hook patterns, reviewing and fixing extension point anti-patterns in Directory.Build files, fixing missing Exists() guards on imports that break fresh clones, fixing NuGet package hooks being silently dropped instead of appended, making build targets extensible for other projects, injecting custom logic into the build pipeline, creating NuGet packages that extend the build, conditionally disabling imports. DO NOT USE FOR: target authoring patterns (use target-authoring), props vs targets placement (use directory-build-organization), general anti-patterns (use msbuild-antipatterns), non-MSBuild build systems.

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Build CarPlay-enabled apps using the CarPlay framework. Use when creating navigation, audio, communication, EV charging, parking, or food ordering apps for the car display, working with CPTemplateApplicationScene, CPListTemplate, CPMapTemplate, CPNowPlayingTemplate, configuring CarPlay entitlements, or integrating with CarPlay Simulator for testing.

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Implement, review, or improve accessibility in iOS/macOS apps with SwiftUI and UIKit. Use when adding VoiceOver support with accessibility labels, hints, values, and traits; when grouping or reordering accessibility elements; when managing focus with @AccessibilityFocusState; when supporting Dynamic Type with @ScaledMetric; when building custom rotors or accessibility actions; when auditing a11y compliance; or when adapting UI for assistive technologies and system accessibility preferences.

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Inspects URL paths and proposes, tests, orders, and applies project-level path cleaning rules so dynamic segments (numeric IDs, UUIDs, slugs, dates) collapse into readable aliases. Use when the user says "clean the paths", "normalize URLs", "group similar pages", "too many distinct paths", "/users/123 and /users/456 are the same page", "set up path cleaning", or asks why a Web analytics or Paths breakdown is fragmented across thousands of nearly-identical URLs. Covers regex syntax (re2), alias placeholder convention, rule ordering, the test workflow, and applying rules via the project-settings-update MCP tool.

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。

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.

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。

End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestrating cutadapt primer removal, per-run DADA2 ASV inference (learnErrors/mergeSequenceTables/removeBimeraDenovo), region-matched taxonomy assignment, a SEPP/Greengenes2 tree, alpha/beta diversity at a declared sampling depth (phyloseq/vegan, adonis2 paired with betadisper), compositional DA as a consensus of >=2 tools (ALDEx2/ANCOM-BC2) on unrarefied counts, and optional PICRUSt2 functional prediction gated on NSTI. Covers the stage-ordering decisions (primers before truncation, per-run error model, rarefy for diversity not DA, predicted potential not activity) and defers each per-step choice to the six microbiome skills. Use when staging an amplicon study end to end or chaining ASV inference, taxonomy, diversity, and differential abundance. For shotgun reads see workflows/metagenomics-pipeline.

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End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering, why Kraken2 read counts are not abundances and MetaPhlAn cell fractions do not equal Bracken read fractions, and the consistent-pipeline framing. Use when profiling shotgun metagenomic samples end to end, or chaining classification, abundance, and function. For resistome see metagenomics/amr-detection; for strains see metagenomics/strain-tracking; for assembly see genome-assembly/metagenome-assembly.

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。