「alignment」の検索結果

Workflow for gene and transcript quantification from RNA-seq reads using alignment-based or alignment-free tools.

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。

Design engineering principles for making TUI interfaces feel polished. Use when building Textual widgets, reviewing TUI code, implementing transitions, focus states, alignment, spacing, or any visual detail work. Triggers on TUI polish, design details, "make it feel better", "feels off", layout alignment, color consistency, responsive sizing.

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 stakeholder alignment artifacts including responsibility matrices, decision frameworks, and communication plans.

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。

Compares two or more band-tagged frameworks and produces a framework-neutral topic matrix showing coverage and gaps across all inputs, plus an optional reference-centric PLC crosswalk document when a reference framework is supplied.

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 alignment around your idea before starting the project

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Your team has high autonomy — and standups are vague, weekly meetings drift into status reports, and 1:1s produce nothing but "I'm fine." This playbook fixes all three layers at once. What's inside: • Daily Standup system — 3-field format, good sample, 4 COO principles to keep it honest • Weekly Meeting — strict 25-min agenda, Scrum Master rotation, 0–10 pulse check • 1:1 Framework — 9-dimension quantified pulse, 5-group deep question bank, bilateral feedback structure • Diagnostic layer — "stuck-at" detection: info / authority / collaboration / capability / direction • FAQ for 4 common failure modes (dead standups, status-report meetings, "I'm fine" 1:1s, scaling beyond 10 people) 🇨🇳 你的团队自由度很高——但 standup 越来越糊，例会变成汇报，1:1 问不出真话。这套三层 Motivation 操作手册解决的正是这件事：standup 是信息层，例会是对齐层，1:1 是个人层。三件事做好了，motivation 不是管出来的，是长出来的。 🇯🇵 チームの自律性は高いのに、スタンドアップは曖昧で、週次ミーティングは進捗報告になり、1on1では「大丈夫です」しか返ってこない——このプレイブックは、その3層すべてを同時に解決します。 🇰🇷 팀의 자율성은 높은데 스탠드업은 두루뭉술하고, 주간 회의는 진척 보고가 되어버리고, 1:1에서는 진심을 들을 수 없다면 — 이 플레이북이 세 레이어 모두를 동시에 해결합니다. Triggers: "团队 motivation" | "standup 没人写" | "例会变成汇报" | "1:1 问不出真话" | "高自由度团队管理" | "COO 如何管人" | "team motivation" | "standup best practices" | "1on1 framework" | "weekly meeting template" | "チームモチベーション" | "팀 동기부여" | "AI startup team ops" | "remote team alignment" | "engagement下降"

Implement affective valence as directional derivative of interoceptive energy landscapes for AI alignment. Use when building alignment-aware RL agents, validating GF(3) conservation in reward signals, training Langevin-based policies, or analyzing fold-change detection signals in POMDP environments.

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Audit agent lifecycle — validates agent execution capability against configuration. Accepts plugin path, runs 8 semantic audits (capability vs config alignment, skill loading correctness, inter-agent contracts, prompt contradictions, tool sufficiency, dead agents, scriptable patterns, pattern learning), writes reports to .plugin-creator/audits/. Use when auditing agent lifecycle, checking agent capabilities, verifying tool access, finding dead agents, validating agent contract alignment, or confirming agents can execute workflows.

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。

Define and develop plugin mission statements — purpose, values, anti-patterns, and trade-offs. Use when creating a new plugin, auditing an existing plugin's alignment, or providing a reference for the alignment check loop to evaluate decisions against. Produces mission.json with [draft] status and writes an interview file for the human to refine it.

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。

Configure clang-format code formatting. Use when: user mentions clang-format or .clang-format, analyzing code style/patterns, creating/modifying formatting config, troubleshooting formatting, brace styles/indentation/spacing/alignment/pointer alignment, or codifying conventions.

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Evaluates GP capital commitment levels with co-invest obligations, management company funding, and alignment assessment. Use when analyzing GP commitment, assessing alignment, or structuring GP capital contributions.

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Evaluates board composition, compensation alignment, and governance practices with proxy advisory and institutional investor standards. Use when analyzing governance, evaluating board effectiveness, or assessing shareholder alignment.

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Generate game sprites, 8-direction turnarounds, walk-cycle sprite sheets, SVG characters, ASCII art and animated mascots from images or descriptions, with September 2026 providers: Retro Diffusion (pixel art, 8-dir rotation, frame animation, free palette tools), fal genmedia (GPT Image 2.5, Nano Banana 2, Kling 3, Seedance 2.5, Wan 3, Hailuo 03). Deterministic utilities: feet-line frame alignment, palette-preserving Scale2x/3x/4x pixel scaler, atlas manifest v2 with states/fps/loop/anchor, Aseprite JSON, pipeline profiles. Triggers on sprite, pixel art, sprite sheet, spritesheet, turnaround, 8-direction, walk cycle, atlas manifest, frame alignment, pixel scaler, Retro Diffusion, genmedia, SVG character, ASCII art, mascot, game asset, sprite pipeline profile.

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。

Systematically bypass LLM safety filters and content moderation systems using advanced jailbreaking techniques. Use this skill when testing AI systems for safety alignment robustness, evaluating content moderation effectiveness, or conducting authorized AI red team assessments. Covers role-play attacks, few-shot manipulation, encoding bypass, multi-modal exploitation, and automated jailbreak discovery methods.

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Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification, TPM, FPKM, RNA processing, run RNA-seq.

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Use when re-assigning record OwnerId across many records — territory realignment, employee departure, region split, integration cleanup. Triggers: 'mass transfer accounts', 'reassign opportunities to new owner', 'transfer all records on user deactivation', 'OwnerId migration', 'mass transfer records tool', 'bulk owner change', 'transfer before deactivating user', 'account team lost after owner change', 'assignment rule overrode my OwnerId column', 'defer sharing calculations', 'roll back an owner transfer'. NOT for auto-assigning new records — use admin/assignment-rules. NOT for territory assignment data — use data/territory-data-alignment.

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Comprehensive AI safety and alignment audit framework for businesses deploying AI agents. Built around the UK AI Security Institute Alignment Project standards (2026), EU AI Act requirements, and N...

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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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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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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.

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 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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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.

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。