「across」の検索結果

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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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedtools genomecov, deepTools bamCoverage/bamCompare/bigwigCompare, bedtools unionbedg, and UCSC bedGraphToBigWig. Covers why a raw coverage bedGraph is not comparable across samples until normalized, the CPM/RPKM/BPM/RPGC normalization menu and the conserved-total assumption that makes them wrong under a global perturbation, the strict sorted-non-overlapping-chrom.sizes bedGraphToBigWig contract that silently corrupts a bigWig, effective-genome-size selection, and bin-size aliasing. Use when building or normalizing a coverage/signal track from a BAM, comparing tracks across samples or conditions, converting bedGraph to a browser-ready bigWig, or diagnosing a track that looks plausible but reports wrong heights.

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Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and transfer-vs-de-novo validation. Use when annotating a new assembly of a species with an existing reference, harmonizing coordinates across builds, or mapping annotations across related species.

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Runs JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens; Allen et al 2019 Genome Research) which models per-sgRNA log-fold-change as the product of a treatment-dependent gene-essentiality term and a treatment-independent guide-efficacy term. Covers the Bayesian decomposition math, the hierarchical efficacy prior shared across screens performed with the same library, when JACKS outperforms MAGeCK (multi-screen joint analysis, libraries with broad efficacy variance) and when it does not (single screen, novel libraries with no prior efficacy), library-reuse efficacy transfer, downstream essentiality interpretation, and the 2.5x sample-size reduction enabled by efficacy-aware testing. Use when running multiple screens with the same library, when guide-level noise is suspected to dominate per-gene signal, when reusing published essentiality reference screens for efficacy priors, or when comparing screens performed across cell lines that share library but differ biologically.

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Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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Estimates SNP heritability and partitions it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.

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Audit and harden your SaaS tool stack — enforce SSO, review OAuth grants, manage shadow IT, and secure admin accounts across Slack, GitHub, Google Workspace, and AWS. Use when tightening security across company SaaS tools.

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Build responsive, mobile-first layouts using fluid containers, flexible units, media queries, and touch-friendly design that works across all screen sizes. Use this skill when creating or modifying UI layouts, responsive grids, breakpoint styles, mobile navigation, or any interface that needs to adapt to different screen sizes. Apply when working with responsive CSS, media queries, viewport settings, flexbox/grid layouts, mobile-first styling, breakpoint definitions (mobile, tablet, desktop), touch target sizing, relative units (rem, em, %), image optimization for different screens, or testing layouts across multiple devices. Use for any task involving multi-device support, responsive design patterns, or adaptive layouts.

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When the user wants to plan content marketing across channels, define content types and formats, or create a content repurposing strategy. Also use when the user mentions "content marketing strategy," "content types," "content formats," "content repurposing," "content calendar," "content mix," "owned content," "content distribution," "content funnel," or "content planning across channels." For SEO calendar, use content-strategy.

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Given a Japanese NLP GitHub repo/model/dataset (URL / owner/repo / tool name) OR a topic, find what's already in awesome-japanese-nlp-resources and discover related resources NOT yet listed (contribution candidates). Mines the bundled dataset, then expands via web research across GitHub and Hugging Face. Use when the user names a SPECIFIC repository, model, or tool and wants alternatives/equivalents, OR wants to discover Japanese NLP resources for a topic that are NOT yet in the list, OR wants to prepare a contribution. Trigger phrases include 'mecabに似たツール', 'fugashiの代替', 'alternatives to fugashi', 'repos like manga-ocr', 'what else is like sudachi', 'リストに無い新しい日本語NLP', 'awesome-japanese-nlpに追加できそうな', '最近公開された日本語NLPツール', 'find unlisted Japanese NLP repos', 'new Japanese models on Hugging Face', 'contribute a new resource'. For a simple lookup of what already exists, use the search skill instead.

Compare several Japanese NLP libraries, models, or datasets for a keyword (a specific tool name, or a function/task like '形態素解析') across a handful of criteria chosen for that comparison, rendered as a ○/△/✕ table. Use when the user wants a side-by-side comparison of multiple Japanese NLP tools/libraries/datasets, not just the single best one. Trigger phrases include 'X と Y と Z を比較して', '形態素解析ライブラリを比較', 'MeCab と Sudachi どっちがいい', 'どのツールを使うべき', 'compare japanese tokenizers', 'mecab vs sudachi vs janome', 'which embedding model should I use', '日本語NERライブラリの比較表', 'pros and cons of japanese OCR tools'. For a single ranked list use search; for alternatives to one specific tool (or contribution candidates) without a multi-axis table, use discover.

Validate a third-party control repo across four automated layers plus one printed manual recipe. Layer 1 asserts native-source structure (Android getName() and iOS +moduleName to manifest nativeModule; @ReactMethod / RCT_EXPORT_METHOD to methods; no @ReactModule) plus load/init readiness (ReactPackage public no-arg constructor, iOS [cls new] no-arg init, requiresMainQueueSetup NO, non-throwing eager construction), so launch-time crashes surface before any build. Layer 2 validates the committed `./manifest.json` against the ppmplugin-format rules. Layer 3 asserts request/response/error-code agreement across native and PCF. Layer 4 compiles the PCF (auto-skipped if absent). Layer 5 prints a device end-to-end recipe. Native compile belongs to /build-android-binary and /build-ios-binary — this is the cheap structural pre-flight before those slow builds. Reports pass/fail per layer with a fix hint and updates .extension-state.md.

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Review the portfolio across existing engagement records. Use for status across customers; requires accessible permitted records and does not create missing client histories.

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Cross-format content adaptation. Turning one substantial piece into many derivative formats (blog series, email sequences, social posts, webinars, podcasts, video shorts) without losing the original's value or producing AI-slop variants. The discipline of adaptation per medium rather than mass-blast distribution. Triggers on content repurposing, content adaptation, cross-format content, content atomization, content multiplication, content distribution across formats, source-piece-to-derivative, video shorts from blog, email from whitepaper, podcast from article, blog series from research. Also triggers when a flagship piece is shipping but the team has not planned how to extend it across formats, when repurposing is happening but the derivatives feel mass-produced, or when AI-assisted repurposing is producing slop variants of strong source pieces.

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Diagnose performance issues on Amazon SageMaker HyperPod clusters — uneven NCCL bandwidth across nodes and poor filesystem throughput. Read-only. Surfaces host-side signals (Xid, ECC, NVLink, EFA reachability, FSx saturation) and routes to the appropriate sibling skill (hyperpod-node-debugger, hyperpod-nccl, hyperpod-version-checker, hyperpod-issue-report) for any remediation. Triggers on uneven NCCL across nodes, straggler node, FSx slow, checkpoint slow, dataloader slow, filesystem bottleneck, FSx throughput, cross-AZ latency, topology mismatch.

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Sanctions and export control analysis tool for Claude Desktop. Real-time individual screening across 30+ official lists (UN, EU, OFAC, OFSI, French DGT...), sectoral analysis, dual-use goods (EU Reg. 2021/821), US/China extraterritorial regimes (EAR, ITAR, FDPR, ECL), USD/SWIFT risk and jurisdictional mapping across 30+ countries. All results sourced and verified in real time — no memory-based answers. Responds in French, English, German, Spanish, Russian and Chinese. Updated 19 May 2026 (EU 20th package, UK SEUC, Cuba EO). Indicative guidance only — not legal advice.

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Guide to analyze multiple documents (PDF, DOCX) against user-defined columns and produce a structured Excel output with citations. Use when the user wants to: (1) Extract specific information from multiple documents into a table, (2) Compare clauses or provisions across contracts, (3) Create a document review matrix with source citations. Triggers on: 'tabular review', 'document matrix', 'extract from documents', 'compare across documents', 'review multiple contracts'.

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Turns a legal question, a set of draft questions, or source material such as a statute, jury instruction, rubric, contract checklist, or coding manual into a battery of narrow questions that TypeSafe's Jev, a fast classifier that returns probabilities rather than prose, can answer reliably across many documents. The skill breaks conclusions such as negligence, felony murder, or standing into element-level questions, writes the governing rule into each question, and delivers the questions alone, in Jev's request format or in plain English. Built for legal work that asks the same questions of many texts: coding statutes across jurisdictions, coding opinions or case files for empirical research, checking contracts against a review checklist, screening intake narratives, and grading student work against a rubric. Use when asked to write Jev questions, build a classifier for legal documents, or turn a legal test into yes-or-no questions. Running the questions requires Jev access; writing them does not.

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Research a US employment law topic across federal, state, and city jurisdictions and produce structured research notes with proper source attribution. Use this skill any time the user asks about US employment laws, regulations, or pending legislation - from a single jurisdiction question to a 50-state survey. Triggers include phrases like "research [employment law topic]", "what are the laws on [employment topic]", "state-by-state [employment topic]", "help me understand [topic] across the US", or any prompt that asks for a legal landscape overview before another deliverable. Always run this BEFORE the employment-law-dashboard skill if a dashboard is the eventual output. Output is a structured research note that distinguishes primary sources (statutes, regs, agency guidance) from secondary sources (law firm alerts, tracker orgs).

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When you want to manage projects across your businesses using a kanban + Eisenhower methodology. One kanban per business (whatever portfolio of businesses, projects, or initiatives you run). Tool-agnostic — connects via API/MCP to whatever PM tool each business uses (Notion, GitHub Projects, Plane, Linear, Obsidian file-based, or manual mode). Async-first output. Six modes — setup (scaffold a new board for a business), triage (Eisenhower-sort the backlog), next (pick the next thing to work on, single board or across all), status (paste-ready async snapshot), unblock (diagnose Review/Blocked column), weekly (Friday pulse + week planning). Triggers on "/pm," "/pm setup," "/pm triage," "/pm next," "/pm status," "/pm unblock," "/pm weekly," "what should I work on next," "kanban status," "Eisenhower this," "triage my backlog," "what's blocked."

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The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across

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Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

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Build a brand's messaging hierarchy — taglines, value propositions, key messages, and proof points for each audience. Use when the user says "brand messaging", "messaging framework", "value proposition", "tagline", "brand tagline", "key messages", "messaging hierarchy", "what should we say about our brand", "brand copy foundation", "messaging architecture", "elevator pitch", "one-liner", "brand statement", or needs consistent language across all communications. Also use when messaging feels inconsistent across channels or teams.

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