「route」の検索結果

Performs set operations on genomic intervals - intersect (-wa/-wb/-wo/-wao/-loj/-c/-v/-u), subtract (-A), merge (-d, -c/-o), complement, cluster, multiinter, unionbedg, map, and groupby - with bedtools (CLI) and pybedtools/pyranges/bioframe (Python). Covers the sorted-input contract and the -sorted chromosome-order footgun, reciprocal/fractional overlap (-f/-F/-r/-e) and the A-vs-B asymmetry, -split for spliced/BED12/BAM features, and jaccard/fisher as mechanics only. Use when finding overlapping or unique regions between BED/peak/feature files, building consensus peaksets, removing blacklisted regions, transferring annotation values onto intervals, or computing interval-set similarity; route overlap-significance testing to overlap-significance.

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Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected with cooltools (expected_cis per-diagonal P(s), expected_trans scalar), builds observed/expected (O/E) matrices, and diagnoses polymer state from the P(s) log-derivative. Covers the within-matrix-vs-cross-sample distinction (balancing is NOT a normalizer), the equal-visibility assumption that CNV/aneuploidy violates (use raw counts for copy-number), cis-only balancing, mad_max/blacklist masking before balancing, multiplicative cooler weights vs divisive juicer weights, and the resolution-vs-depth budget. Use when balancing a .cool/.mcool, computing expected or P(s), making O/E matrices for compartments/loops, deciding ICE vs KR vs SCALE, choosing a resolution for a given depth, or troubleshooting NaN/all-NaN balanced matrices; route cross-sample comparison to hic-differential.

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Detects TAD boundaries from balanced Hi-C contact matrices via the diamond-window insulation score (cooltools insulation) and HiCExplorer hicFindTADs, returning a continuous log2 insulation track, valley-prominence boundary_strength, and Li/Otsu-thresholded is_boundary flags across a list of window sizes. Covers the multi-scale window sweep (sub-TAD to compartment-domain), why the boundary is reproducible but the domain partition is not, cross-condition comparison via differential SCORE not differential partition, and the insulation-vs-compartment orthogonality. Use when calling TADs or domain boundaries, computing insulation scores, choosing a window size, ranking boundary strength, comparing boundaries across conditions, or annotating CTCF-backed boundaries; route domain rendering to hic-visualization and boundary-feature overlap to genome-intervals.

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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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Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046), MeTPeak (HMM over sliding windows; Cui 2016 *Bioinformatics* 32:i378), MACS3 / MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment confirmation via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output formats, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union; cross-caller IDR-equivalent), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody-based methods cannot resolve, and orthogonal-validation routes (miCLIP / GLORI / m6A-SAC-seq / m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set as a whole, reconciling differing peak sets across tools, validating MeRIP peaks against orthogonal single-base methods, interpreting peaks at the 5' end where m6Am contamination is possible, or recommending a multi-tool consensus strategy.

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 users need bioinformatics analysis on the NCPGR cluster, especially when converting analysis requests into local software choices, resource plans, and LSF job scripts.

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 this skill when the user asks about oversize / overweight load permits — state-by-state permitting process, escort vehicle (pilot car) requirements, route surveys, federal axle weight limits (Federal Bridge Formula), holiday restrictions, multi-state permits, and how to determine if a load needs a permit. Reference state DOT permitting offices.

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Use when discussing the mobile apps drivers use day-to-day — load boards (DAT, Truckstop), route planners (Trucker Path, CoPilot Truck), expense and per diem apps (Per Diem Plus), parking apps (Park My Truck), maintenance / DVIR apps, and how these stack with the carrier's ELD app.

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The TTS/STT/audio-playback system behind the one `speak()` entry point. Use when working on read-aloud, the Listen panel, voice/speed settings, transcription, mic capture, SpeakerButton, iOS playing silence, audio API routes, or files in features/audio/, features/tts/, hooks/tts/, app/api/audio/.

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 adding/changing a CMS surface manifest, the site_structure/html_pages_structure framing XML, a CMS context menu/extraSections wiring, or the cms-authoring platform skill. Also use when a new CMS route/tab needs an agent entry point.

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Recipe for THE DOOR LAW (every record the UI names opens; every detected problem ships its fix) and THE INVENTORY LAW. Use before building or fixing a surface that names a record or flags a problem (cell, row, dialog, badge, warning, id, count), or on 'no link to X', 'why can't I click this', 'dead end', EntityRef, peek. NOT for page chrome (use core-route-headers).

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One-route pattern: public marketing landing plus signed-in workspace. Use when creating or fixing a landing page or a feature's front door, guests see an error, 'make /X work signed out', signed-in users land on a pitch, or ModuleLanding / AuthedWorkspaceCTA. NOT for (public) share viewers or free tools.

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。

Continuous localhost UI iteration loop with Arman, through full surface certification. Use when he asks to fix, refine, review, or iterate on a page, route, panel, overlay, or other UI while he may inspect localhost. NOT for a report-only UI audit.

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。

Super-Admin-only lock-down pattern. Use before touching admin.admins, admin.admin_audit_log, is_super_admin() / requireSuperAdmin() / selectIsSuperAdmin, app/api/admin/admins/**, app/(admin)/administration/users/admins/**, the admin RPCs (admin_promote, admin_update, admin_revoke, admin_list, admin_list_audit, admin_find_user_by_email), createAdminClient(), a new RLS policy, SECURITY DEFINER RPC, or admin-gated route, or when locking a sensitive table to Super Admin.

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。

Decision-ready scouting record for a user-connected provider access campaign. Use when an assigned Provider Access Launch task needs its easiest official route, minimum scopes, cost, account needs, approval path, implementation consumer, and easy-execute verdict established before submission. NOT for client Local Listings distribution.

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Entry point and shared rules for structural changes to the live Matrx database. Use before any DDL: dropping, merging, or renaming a table, changing a function, RPC, trigger, or policy, hunting straggler tables, or starting a deprecated, schema move, or canonicalization (it routes to those skills).

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。

Admin debug system wiring for the floating AdminIndicator's live debug data and Copy Full Context. Use when adding debug visibility to a route or feature, wiring useDebugContext or the debug panel, capturing console errors, or enabling the copy-context workflow for a page.

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The matrx-frontend side of the matrx-extend Chrome extension bridge. Use when adding or changing a FRONTEND_RPC action handler, a window-panels deep-link the extension opens, a headless API route it calls, or debugging a silent chrome.runtime.sendMessage or Broadcast round-trip. NOT for code in matrx-extend, matrx-local, or aidream (each has its own connect-* skill).

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Routes general Convex requests to the right project skill. Use when the user asks which Convex skill to use or gives an underspecified Convex app task.

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Integrate Convex static self hosting into existing apps using the latest upstream instructions from get-convex/self-hosting every time. Use when setting up upload APIs, HTTP routes, deployment scripts, migration from external hosting, or troubleshooting static deploy issues across React, Vite, Next.js, and other frontends.

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Security review checklist for Convex functions, auth logic, public queries, admin routes, webhooks, uploads, components, and AI-generated code. Use when reviewing code that touches user data, PII, or access control, or before any deploy of an app with auth.

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。

Security review checklist for Convex functions, auth logic, public queries, admin routes, webhooks, uploads, and AI-generated code. Use when reviewing code that touches user data, PII, or access control.

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Convex is the backend agents get right on the first try: an all-TypeScript reactive platform where the database, server functions, scheduling, file storage, auth, and realtime sync are one type-safe system, every function is a transaction, and `tsc` catches most mistakes before deploy. Ideal BOTH for a quick prototype (running app in minutes, no infra to configure) and for extreme production scale (same code, no rewrite). Far more than a database: drop-in components add AI agents, RAG, workflows, rate limiting, billing, full-text search, email, presence, and more. Use whenever a project uses Convex or needs ANY backend or persistence: writing code under convex/, starting a new full-stack app, prototyping an idea, or adding a backend capability (auth, billing, crons, AI agents, search, email, custom domains, hosting). Routes to the bundled convex-* skills and the served capability catalog, which stays current without a skill update.

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Master skill for Abaqus FEA scripting. Use for any finite element analysis, topology optimization, or Abaqus Python scripting task. Routes to appropriate specialized skills.

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。