「alignment」の検索結果

Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, taking raw mzML to a feature table via CentWave peak detection, retention-time alignment, peak-density correspondence, gap-filling, CAMERA redundancy collapse, and built-in QC feature filtering. Use when converting centroided LC-MS runs into a features-by-samples matrix and deciding centWave/grouping/alignment parameters. For drift correction and QC/CV filtering execution see metabolomics/normalization-qc; for metabolite identification see metabolomics/metabolite-annotation; for the MS-DIAL GUI alternative with MS2Dec deconvolution see metabolomics/msdial-preprocessing; for downstream statistics see metabolomics/statistical-analysis.

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Windows アプリ開発 (Fluent Design / WinUI 3) の デザインガイドラインリファレンス。 layout, spacing, alignment, elevation, geometry, breakpoints, Color, Mica, Acrylic, Smoke, Reveal Highlight, materials, typography, Segoe Fluent Icons, app icons, motion, easing, connected animation, page transitions, parallax, reduce motion, NavigationView, TabView, CommandBar, menus, keyboard accelerators, access keys, accessibility, high contrast, RTL, globalization, widgets design。

Rive アニメーションランタイムリファレンス。 Rive クラス、useRive、useStateMachineInput、RiveComponent、 State Machine、Data Binding、ViewModel、ViewModelInstance、Events、 Layout / Fit / Alignment、.riv ファイル読み込み。 @rive-app/canvas、@rive-app/webgl2、@rive-app/react-canvas、@rive-app/react-webgl2。 Rive Scripting API (Luau)、Artboard、Property、Path / Paint / Renderer、 WGSL Shaders、GPU pipeline、Node / Layout / Converter スクリプト。

リファクタリング（構造変更）と機能変更（behavior change）が同一 diff に混在していないかを識別し、structural change に対する external behavior preservation の証拠（テスト・型・静的解析）が揃っているかを diff-time で確認する。証拠不足のときは Characterization Test 追加を促すか question とする。DTO/公開 API の破壊的変更検出は api-compatibility、完了主張の反証や抽出リファクタの性能特性退行は refactor-claim-audit、新知識の命名・責務・境界への反映は knowledge-to-code-alignment、投機的抽象化・スコープ逸脱は altitude-generalization / fix-scope-integrity へ委譲する

Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.

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Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.

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Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.

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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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Layout structure for web interfaces, from grouping and alignment to reading order, progressive disclosure, and adaptive breakpoints. Use when structuring a page or component, spacing or aligning controls, deciding what collapses at small sizes, handling RTL layout direction, or reviewing frontend code for layout. Triggers on layout, spacing, alignment, grouping, negative space, whitespace, visual hierarchy, reading order, progressive disclosure, breakpoints, responsive layout, container queries, safe area, full-bleed, edge-to-edge, layout margins, RTL layout, logical properties.

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Simple Preference Optimization for LLM alignment. Reference-free alternative to DPO with better performance (+6.4 points on AlpacaEval 2.0). No reference model needed, more efficient than DPO. Use for preference alignment when want simpler, faster training than DPO/PPO.

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Fast tokenizers optimized for research and production. Rust-based implementation tokenizes 1GB in <20 seconds. Supports BPE, WordPiece, and Unigram algorithms. Train custom vocabularies, track alignments, handle padding/truncation. Integrates seamlessly with transformers. Use when you need high-performance tokenization or custom tokenizer training.

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Complete OKR & Strategy Execution system — from company vision to weekly execution. Covers goal hierarchy, OKR writing methodology, scoring rubrics, alignment cascading, KPI dashboards, review cadences, team accountability, and quarterly planning rituals. Use when setting goals, running planning cycles, tracking OKRs, building KPI dashboards, running retrospectives, or aligning team work to strategy. Trigger on: "OKR", "objectives", "key results", "goal setting", "quarterly planning", "KPIs", "strategy execution", "annual planning", "team goals", "alignment", "review cadence", "what should we focus on", "prioritize", "goal tracking", "north star metric".

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Full website audit for ICP alignment, messaging clarity, conversion optimization, and trust signals

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Perform evidence-backed impact analysis before changing code, data, interfaces, or governance documents, then compare the planned impact with the actual diff after implementation. Covers call paths, data and schema, API contracts, tests, documentation, ADRs, deployment, migration, and rollback. Use for cross-module or high-risk changes, database migrations, authentication, public interfaces, blast-radius questions, pre-change checks, and post-implementation alignment.

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Blenderのキャラクターやアニメーションを、骨格・座標・接地状態などのデータと画像で検査し、足滑り、向きの不一致、ねじれの原因と修正点を整理するスキル。

• 歩行時の足滑りや床へのめり込みの確認
• キャラクターの向きと進行方向の比較
• 別の骨格へ動きを移した後の姿勢検査

採点済みの競合情報を、市場マップや比較表、差別化の余地、優先施策を含むレポートにまとめます。経営層への報告や、チームで競争方針を決める場面に役立ちます。

• 経営層や取締役会向けの競合報告
• 完成済み競合プロフィールの統合
• 差別化の余地と競合脅威の検討

Reference-free preference alignment, simpler than DPO.

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Run the CCS Align seat's hourly breathing cycle — prove the local claude-mem worker is healthy, pull needle observations through search → timeline → get_observations, land them in a seat-owned middle cache via atomic grab → append → filter exclude-marks → replace, manage exclude marks, and walk house → project → seat rules to detect conflicts (SHADOW_HOUSE, DENY_ALLOW, DRIFT, CLOCK_HEADER) with an append-only rules-report.md. Use when asked to run CCS Align, breathe the alignment seat, refresh the middle cache, exclude or restore an observation, walk rules, check rules conflicts, or check the Worker Watch board.

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Use when the user wants to design, redesign, shape, critique, audit, polish, clarify, distill, harden, optimize, adapt, animate, colorize, extract, or otherwise improve a frontend interface. Covers websites, landing pages, dashboards, product UI, app shells, components, forms, settings, onboarding, and empty states. Handles UX review, visual hierarchy, information architecture, cognitive load, accessibility, performance, responsive behavior, theming, anti-patterns, typography, fonts, spacing, layout, alignment, color, motion, micro-interactions, UX copy, error states, edge cases, i18n, and reusable design systems or tokens. Also use for bland designs that need to become bolder or more delightful, loud designs that should become quieter, live browser iteration on UI elements, or ambitious visual effects that should feel technically extraordinary. Not for backend-only or non-UI tasks.

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Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.

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。