「maps」の検索結果

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.

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。

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.

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。

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.

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。

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.

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。

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.

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。

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.

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。

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.

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。

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.

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。

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.

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 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).

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。

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

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。

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

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。

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

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 for ethical thinking, or when a plan could harm or unfairly burden people: "should we do this?", "is this fair?", "privacy or bias risk", "who gets hurt?". Maps stakeholders, harms, power and consent. Skip for legal advice, neutral fact lookups and implementation-only work.

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 for systems thinking, or when a change may ripple beyond its target: "what are the side effects?", "why does this keep coming back?", "how do these teams or services affect each other?". Maps loops, delays and leverage points. Skip for single-step fixes.

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。

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

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。

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

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。

Guides continuous improvement and change management for SMEs adopting AI. Applies Marginal Gains philosophy, Kaizen principles, and structured sprint methodologies to organizational transformation. Use when user asks about change management, continuous improvement, AI adoption strategy, team resistance, transformation roadmaps, or improvement sprints.

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 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'.

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

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

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 edit editable Excalidraw diagrams in Canvas Notebook through the Scene-Service tools. Use for diagrams, flows, sketches, architecture maps, visual explanations, or requested .excalidraw documents.

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 integrate the machine-level core of a new EMULATORS emulator, including Computer and Emulator derivatives, memory and port maps, chip ownership and wiring, clock coordination, model configuration, commands, formatters, executables, and Visual Studio projects. Use when scaffolding a machine namespace, adding a model or regional variant, assembling existing components into a computer, or making a new emulator build and start.

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。

Project-orientation workflow (/orient): installs predicate's enforcement into a target project, maps its structure and goal, and authors the persistent conditioning layer (AGENTS.md goal-hierarchy) so every subsequent walk is anchored and gated. Trigger when: - Onboarding a new project into predicate for the first time. - Refreshing an existing project's AGENTS.md hierarchy against the current state of the repository (re-run = refresh). - Prompt contains: /orient, orient workflow, onboard project, project orientation, AGENTS.md hierarchy, persistent conditioning layer.

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。