'maps' 검색 결과

Establish, author, restructure, or audit human-first processor Architecture, Design, Research, Review, and Verification documentation. Use for progressive documentation scaffolding, authority maps, reading paths, document-type content contracts, length-budgeted splitting, or maintainability reviews. Do not use as a substitute for cycle-accurate microarchitecture analysis or RTL implementation.

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Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.

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Plot per-gene mutation distributions on a protein-domain map (lollipop / needle plots) showing mutation position, recurrence count, and variant classification with maftools, g3-lollipop, trackViewer, and ProteinPaint. Use when visualizing recurrent mutation hotspots on a single gene's protein, marking domain boundaries from UniProt/Pfam, comparing missense vs truncating distributions, or contrasting two cohorts on the same lollipop.

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Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA targets from indirect, integrating CLIP-derived target maps with TargetScan / miRDB / DIANA predictions, applying canonical 7mer-8mer seed matching with 3' UTR context, or recovering miRNA-mRNA chimeras at scale.

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Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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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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Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.

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Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.

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Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.

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Maps test coverage to plan acceptance criteria and flags requirements with no tests. Use during Test/Review phases. NOT for running tests (mk:testing); NOT for structural review (mk:review).

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Analyzes ticket complexity and maps dependencies against an existing codebase before sprint planning. Triggers on 'how complex is this ticket', 'what should we work on first', 'can we fit this in the sprint', 'tech review before planning', 'plan the sprint'. NOT for writing implementation plans (see mk:plan-creator); NOT for scope/ambition review (see mk:plan-ceo-review).

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Connect business positioning to a concrete visual language. Maps strategic positioning (category, differentiator, who-it's-for, who-it's-against) onto visual decisions — palette, type, imagery, tone — so the look reinforces the strategy. Use when the user says "positioning into visuals", "what should the brand look like given our strategy", "align visuals with positioning", or is moving from strategy to brand expression. Part of the Creative Production set.

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Use common CLI, Kali, and shell tools to inspect web Targets, captured assets, logs, HAR/PCAP files, packages, and generated artifacts, then turn observations into Evidence, Security Signals, and ranked Hypotheses. Use when the user asks for web bug-hunting inspection, digital records, URL maps, crawling, endpoint discovery, JS bundle/package analysis, light forensics, or command-line investigation workflows.

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Workflow Phase 2 — Codebase Scouting and Constraint Discovery. Maps the relevant slice of the codebase for a given task. Produces a scout report at `docs/scout/<slug>.md` naming the files, modules, and patterns the proposed work touches or constrains. Report decisions execute in main context with full conversation visibility; gathering MAY be delegated to read-only advisory subagents (seed.md §4.2-A).

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Geocode, POIs, routes, timezones via OpenStreetMap/OSRM.

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Analyze competitor strategies, content, pricing, ads, and market positioning across Google Maps, Booking.com, Facebook, Instagram, YouTube, and TikTok.

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Analyze market conditions, geographic opportunities, pricing, consumer behavior, and product validation across Google Maps, Facebook, Instagram, Booking.com, and TripAdvisor.

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2D game development principles. Sprites, tilemaps, physics, camera.

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Analyze competitor strategies, content, pricing, ads, and market positioning across Google Maps, Booking.com.

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Use when authoring or rewriting a roadmap in agents/roadmaps/ — phases, goal, acceptance criteria, council notes; fires even on 'write a plan for X' / 'draft a roadmap'.

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Use when looking for project-specific documentation. Knows which docs exist in agents/reference/docs/ and agents/settings/contexts/ and maps work areas to relevant docs.

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Use when reading, creating, or updating agent documentation, module docs, roadmaps, or AGENTS.md. Understands the full .augment/, agents/, and copilot-instructions structure.

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[Documentation] Use when a workflow step or the user asks for canonical feature specs and test scenarios: author, audit, amend, tests and sync. discovery maps overlaps; clarify confirms decisions; index derives navigation/ERD.

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