「features」の検索結果

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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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CTCF-only/DNase-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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。

Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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Use when a carrier asks how to spec a new tractor — engine choice (X15 vs DD16 vs PACCAR MX), transmission (manual vs automated manual vs automatic), axle ratio, sleeper size, fuel tanks, aerodynamic options, electronic features, warranty, fleet-spec vs premium-spec tradeoffs, and how spec choices affect resale value.

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Use this skill to evaluate document retention software options. Covers compliance features, ease of use, integration, and cost.

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Use when a carrier asks about fuel-card vendor selection (Comdata, EFS, WEX, RTS, Pilot Flying J, Love's Connect), discount levels, fraud control, driver authorization PINs, IFTA reporting features, cash advance, money codes, or how the card fits into payroll/settlement workflows.

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Use when modifying anything under features/files/, app/(core)/files/, app/(public)/share/, or any caller that uploads, downloads, lists, moves, renames, shares, or previews user files.

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The WindowPanel component and Window Manager. Use when a window won't drag/resize/minimize, the tray is missing, window state doesn't persist, rendering `<WindowPanel>` on a page, or editing features/window-panels/** or windowManagerSlice.ts. NOT for opening/registering overlays (use overlay-system).

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Lifecycle for AI Matrx agent-aware UI surfaces. Use when creating a surface in features/surfaces/manifests/, or completing or repairing one that is partial, stubbed, unregistered, missing runtime context or context menus, or not agent-wired. NOT for certifying a surface (use surface-check).

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The Matrx user settings system (SettingsShell, useSetting, tab registry). Use when adding a preference or settings tab, binding a Redux slice to settings, wiring a settings deep link, or touching features/settings, components/official/settings, or components/user-preferences.

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The cross-repo scheduling system (sch_* tables, matrx-scheduler). Use when touching features/scheduling/**, /schedules or /administration/scheduling, migrations/sch_*.sql, a scheduled agent, cron, trigger, lease, or claim, or debugging ghost tasks, missed fires, double-runs, or stuck claims.

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Overlay controller for dialogs, sheets, modals, windows, and toasts opened by dispatch. Use when opening, adding, registering, or debugging an overlay, or touching features/overlays/**, app/DeferredSingletonCore.tsx, lib/redux/slices/overlaySlice.ts, dispatch(openOverlay(...)), useOpenX hooks, or XController components. NOT for the WindowPanel component itself (use window-panels).

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react-resizable-panels v4 rules for this SSR codebase. Use when importing react-resizable-panels (PanelGroup and PanelResizeHandle are v3 names), editing components/ui/resizable* or features/code/layout/, building a split-pane, sidebar, or drag-handle layout, or persisting or toggling panel sizes.

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Cross-app save-to-notes components and patterns. Use when adding save-to-notes to a feature, wiring overlay note capture, editing features/notes/actions/ or its consumers, or using QuickCaptureButton, SaveToScratchButton, SaveSelectionButton, QuickNotesSheet, CategoryNotesModal, or openSaveToNotes.

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。

Workflow for classifying AI Matrx server log lines in features/server-logs/log-rules.ts. Use when examining raw server logs, new [ModuleName] bracket tokens appear unclassified, log categories are wrong, or adding module recognition to the log viewer.

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RichDocument action toolkit for markdown and interactive content outside live chat. Use when adding an action or content source, wiring a remote action surface, putting actions on a MarkdownStream/BasicMarkdownContent preview, or touching features/rich-document/**, <RichDocument>, <RichDocumentActionSurface>, registerAction, ContentSourceAdapter, or enableContextMenu. NOT for the live chat message bar (use overlay-system).

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Doctrine for auditing an ENTIRE feature and building it to its ideal state. Use on 'deep dive on X', 'audit the X feature', 'figure out everything X does', 'take over X and finish it', 'bring X up to best practices', or when a whole feature needs overhauling, unifying, or finishing, not patching. NOT for one small addition (use build-sub-feature).

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Redux state for agent execution and firing agent shortcuts. Use when editing features/agents/redux/, building agent UI, creating a conversation, touching assembleRequest or NDJSON stream state, wiring agent-state selectors, adding a per-conversation capability, or triggering a shortcut from a button, menu, or code (useShortcutTrigger, launchAgentExecution).

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Doctrine for adding a capability INTO a live, existing feature to a world-class bar. Use on 'add X to Y', 'extend Y to support X', a new option, button, setting, endpoint, or tool for Y, or a sub-feature spec to implement. NOT for whole-feature audits or overhauls (use feature-deep-dive).

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Putting a platform feature on the Board (/board) as an Add-menu item with its real component and full agent surface. Use when adding a feature, record type or 'X on the board', or editing features/board/items/** or a tile body.

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Recipe for an agent building a small custom web app (an Applet) for one person or business on THEIR OWN store tables, live at aimatrx.com/applets/<slug>. Use when asked to build an app, portal, calendar, tracker, dashboard screen or client view on someone's tables/data in AI Matrx. NOT for platform features (use build-sub-feature) or tables the platform keeps for itself (defineTypedTable).

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。