「scale」の検索結果

Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (log2 IP/input bigWig via deepTools bamCompare; pyGenomeTracks; Gviz; IGV/UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), feature-distribution stacked bars, and volcano/MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012; Meyer 2012). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features, generating DRACH motif logos as sanity checks, rendering volcano plots of differential m6A, or reproducing the stop-codon enrichment plot.

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 distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when BLAST fails to find homologs that should exist, when working at metagenomic scale (DIAMOND, MMseqs2), or when structure beats sequence (Foldseek). Covers PSI-BLAST (iterative PSSM), jackhmmer (iterative HMM), HHblits/HHsearch (profile-profile), DIAMOND, MMseqs2, and Foldseek (3Di structural alphabet, van Kempen 2024).

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 single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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。

Build publication-quality figures in R with ggplot2 using the grammar of graphics (data + aesthetics + geometries + scales + facets + themes) with CVD-safe palettes, cairo_pdf TrueType embedding, programmatic aes via tidy evaluation, and the theme_classic publication baseline. Use when producing static figures in R for papers, presentations, or reports.

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。

Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows). Use when bulk-pulling genome assemblies, gene metadata across species, ortholog sets, or BLAST databases; when E-utilities are too slow for genome-scale work; or when automatic checksum verification, parallel download, and clean accession-driven retrieval are required. Encodes the JSON-lines output format, dataformat conversion, --dehydrated for cloud workflows, and when Datasets is/isn't the right tool.

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。

Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI) — with scarHRD, and via the whole-genome HRDetect and CHORD models. Covers the genomic instability score, the PARP-inhibitor clinical context, whole-genome-doubling correction, and the scar-versus-state distinction. Use when computing an HRD score for PARP-inhibitor eligibility, deriving LOH/LST/TAI scars from allele-specific copy number, deciding between scar-based and mutational-signature HRD methods, or interpreting an HRD result in a BRCA-reverted or low-purity tumor.

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 base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.

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 positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.

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。

Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma, Schwede & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2021 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

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。

Implement, review, or improve data visualizations using Swift Charts. Use when building bar, line, area, point, pie, donut, or iOS 26 3D charts; when adding chart selection, scrolling, annotations, axes, scales, legends, or foregroundStyle grouping; when plotting functions with BarPlot, LinePlot, AreaPlot, PointPlot, Chart3D, or SurfacePlot; or when creating heat maps, Gantt charts, grouped bars, sparklines, threshold lines, or spatial visualizations.

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。

Writes turn-level tests for a LiveKit agent in the user's normal test suite: pytest (Python) or Vitest (Node.js). Use when the user asks to "write tests for my agent", "add a test for this tool", "test the handoff", "pin this bug", "why does my agent test fail", or after building or changing agent behavior that needs regression coverage. Covers the SDK's test session harness, assertions on messages, tool calls and handoffs, LLM judging of a reply against an intent, mocking tools, multi-turn tests, and judging whole conversations with the built-in judges. For interactive poking use debugging-livekit-agents. For grading whole conversations at scale use running-livekit-simulations.

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。

React composition patterns that scale. Use when refactoring components with boolean prop proliferation, building flexible component libraries, or designing reusable APIs. Triggers on tasks involving compound components, render props, context providers, or component architecture. Includes React 19 API changes.

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。

Speed up local parfor, parfeval, or spmd by switching to a thread-based parallel pool. Trigger when a user describes slow or disappointing local parallel performance, even if they don't mention threads. Symptoms: parfor on a laptop/workstation is slower than expected or "only slightly faster than for"; parfor scales poorly with the number of workers; ticBytes/tocBytes, the Parallel Pool dashboard, mpiprofile, or system tools show large per-worker data transfer; large broadcast variables or sliced inputs make iterations slow; opening a process pool dominates a short workload; user mentions serialisation or data transfer overhead. Also trigger on any question about whether code or a function works on a thread pool. For non-pool MATLAB performance work (vectorisation, preallocation, profiling), defer to matlab-optimize-performance.

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。

AWS EC2 virtual machine management — instances, security groups, key pairs, AMIs, EBS volumes, Auto Scaling Groups, Spot Instances, Session Manager, placement groups, and instance lifecycle automation. Trigger on ANY of these, even when EC2 isn't named explicitly: - Launching or provisioning: "spin up a server", "create a VM", "new instance", "run-instances", mention of instance types (t3, m5, c5, r6, g5, p4d, t4g, c7g, etc.) - SSH / connectivity problems: "connection refused", "connection timed out", "permission denied publickey", "can't connect to my instance", "SSH not working" - Instance management: resize, stop, start, terminate, reboot, change instance type - Cost optimization: stop dev instances overnight, save money on EC2, spot vs on-demand, reserved instances - Auto Scaling: ASG, launch template, mixed instances policy, scale to zero, scheduled scaling - Spot Instances: spot fleet, spot interruption, capacity-optimized, price-capacity-optimized - AMIs and backups: create image, custom AMI, EBS snapshot, DLM lifecycle policy, copy AMI - Monitoring: EC2 CPU utilization, CloudWatch metrics for instance, instance status checks, console output - Access methods: Session Manager, EC2 Instance Connect, bastion host, port forwarding - Security: IMDSv2, instance metadata, IAM role on instance, security group rules - User data and bootstrap scripts, cloud-init

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。

Auto-scale LLM inference clusters on Kubernetes using KEDA, custom GPU metrics, and horizontal pod autoscaling. Handle traffic spikes, implement queue-based scaling, and optimize cost with spot instances for AI workloads.

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。

Manage Azure Virtual Machines and scale sets. Configure availability sets and managed disks. Use when deploying compute resources on Azure.

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。

Deploy, scale, and manage Kubernetes workloads. Create deployments, services, and configurations, manage cluster resources, troubleshoot pods, and implement production-ready Kubernetes patterns. Use when working with Kubernetes clusters, K8s deployments, or container orchestration.

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。

Apply systematic problem-solving techniques when stuck. Use for complexity spirals, innovation blocks, recurring patterns, assumption constraints, simplification cascades, scale uncertainty.

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。

Generate complete, accessible colour palettes from a single brand hex. Produces 11-shade scale (50-950), semantic tokens, dark mode variants, Tailwind v4 CSS output, WCAG contrast checks. Use whenever the user supplies a brand hex and asks for a palette, mentions setting up a design system, wants Tailwind theme colours from a brand colour, or asks to check colour accessibility / contrast.

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。

When the user wants to validate product-market fit, measure PMF, or plan before scaling. Also use when the user mentions "PMF," "product-market fit," "product market fit," "Sean Ellis test," "very disappointed," "vitamin vs painkiller," "PMF validation," "premature scaling," or "validate before scale." For GTM after validation, use gtm-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 Godot 4.7 work must run without a mouse or at scale: batch import of hundreds of GLB props or an AI image-to-3D art drop, naming rules, import presets and post-import scripts, editor plugins, EditorScript and @tool, EditorImportPlugin, GUT or gdUnit4 tests in CI, a GitHub Actions export workflow, GDExtension basics, or a Godot MCP server; also when --import is slow, textures stay uncompressed, tests pass locally but CI fails, or an export ships test folders.

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 sculpting a stylized or cartoon character, bust, collectible or toy in ZBrush (Overwatch, Fortnite, Disney look), judging shape language (S and C curves, parallel lines, 70/30, silhouette read at a distance), exaggerating proportions on purpose, keeping stylized planes crisp through subdivision, sculpting stylized hair (chunky clumps, curve tube strands, ClayPolish), or designing a figure for toy production (articulation, wall thickness, 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。

Use when a task involves game textures or materials through the Scenario MCP: seamless or tileable textures, themed texture packs (brick, wood, stone, floors, hand-painted), PBR materials (albedo, metallic, roughness, normal) on 3D assets, retexturing a mesh, material iteration from reference images, texture upscaling that must preserve tiling, or sizing textures for game engines. Keywords: seamless texture, tileable, PBR, material, retexture, texture upscale, surface.

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。