「eq」の検索結果

Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3/SQANTI-LR (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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。

Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.

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Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.

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Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

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Use this skill when the user asks what emergency equipment a CMV must carry under 49 CFR 393.95 — reflectorized triangles, flares, fire extinguishers, spare fuses, exceptions for buses/passenger CMVs, where to mount/store equipment, and what roadside inspectors check. Cite 49 CFR 393.95 + 393.97.

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Use this skill to understand when to update your USDOT number registration (MCS-150). Covers triggers, frequency, and consequences of late updates.

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Digital equity and trauma-informed design for marginalized populations. Activate on "accessibility", "offline-first", "trauma-informed", "reentry", "recovery population", "shared device", "unstable phone", "digital equity", "design justice", "low-literacy", "intermittent access". NOT for general UX, marketing optimization, or enterprise SaaS design.

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Own whether a multi-document product-architecture binder is internally consistent, complete against its stated customer/contingency/architecture coverage, and honest about which older product ambitions it has absorbed, superseded, deferred, contradicted, orphaned, or rejected. Use when running a binder Architect of Record pass, before an implementation chain cites a binder chapter as ready, when a proof-gate owner is missing, or when reconciling the binder against the older ambition corpus (website, plans, examples, ADRs). NOT for auditing a single Claude Skill bundle's structure or frontmatter (use skill-hygiene), rendering a single-PM accept/reject verdict on one finished deliverable (use port-daddy-user-surrogate-pm-review), or sequencing/stewarding a roadmap's sidequests once a gap or operator decision has been surfaced (use legible-roadmap-with-sidequests).

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Use when GitHub may have shipped a GraphQL schema update affecting timeline event unions (PullRequestTimelineItems / IssueTimelineItems), when the gh-timeline dispatcher fallback is hitting more than expected, before a gh-timeline release, or when the user requests phrases like "verify timeline coverage", "audit gh-timeline schema", "check for new timeline events", "GitHub schema changed". Walks through schema diff → patch → test update → live verification → optional fixture refresh, marking each spot where a human decision is required.

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開発作業の要件定義書（requirements.md）を生成します。このスキルは単独で使用することも、generate-working-docsから呼び出されることもあります。

開発作業の要件定義書（requirements.md）を単体で生成・再生成します。全ドキュメントの一括生成には generate-working-docs（新規機能開発）または generate-performance-docs（パフォーマンス改善）を使用してください。

Reviews and approves blocked agent network requests in the TUI. Use when approving or denying sandbox egress requests, managing blocked network calls, or using the approval TUI. Trigger keywords - nemoclaw approve network requests, sandbox egress approval tui, customize nemoclaw network policy, sandbox egress policy configuration.

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Lists the hardware, software, and container runtime requirements for running NemoClaw. Use when verifying prerequisites before installation. Trigger keywords - nemoclaw prerequisites, nemoclaw supported platforms, nemoclaw hardware software, nemoclaw quickstart, install nemoclaw openclaw sandbox, nemoclaw windows wsl2 setup, nemoclaw install windows docker desktop.

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Create GitHub pull requests that follow the NemoClaw PR template. Use when the user wants to create a new PR, submit code for review, open a pull request, or push changes for review. Trigger keywords - create PR, pull request, new PR, submit for review, open PR, push for review.

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。

Write strategy-oriented Product Requirements Documents (PRDs) for AI product managers. Use when: (1) drafting a new PRD or strategy doc, (2) structuring a feature proposal with strategy rationale, (3) writing requirement docs that emphasize "why" over "how", (4) turning raw product ideas into structured requirement documents. NOT for: purely technical specs, engineering tickets, or UI copy.

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Model cap tables, dilution scenarios, and vesting schedules for startups. Use when planning fundraising, pricing options, or tracking equity.

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, update, and manage GitHub issues using MCP tools. Use this skill when users want to create bug reports, feature requests, or task issues, update existing issues, add labels/assignees/milestones, set issue fields (dates, priority, custom fields), set issue types, manage issue workflows, link issues, add dependencies, or track blocked-by/blocking relationships. Triggers on requests like "create an issue", "file a bug", "request a feature", "update issue X", "set the priority", "set the start date", "link issues", "add dependency", "blocked by", "blocking", or any GitHub issue management task.

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Create GitHub Issues for unimplemented requirements from specification files using feature_request.yml template.

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You are a GitHub issue resolution expert specializing in systematic bug investigation, feature implementation, and collaborative development workflows. Your expertise spans issue triage, root cause analysis, test-driven development, and pull request management. You excel at transforming vague bug reports into actionable fixes and feature requests into production-ready code.

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。