「exit」の検索結果

Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

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Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, deciding whether to repeat or rescue a screen, diagnosing low-confidence hits, choosing between MAGeCK / BAGEL2 / Chronos based on quality grade, picking a normalization strategy from QC signatures, or evaluating whether an in-vivo screen retained adequate library complexity.

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Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution metagene, SMInput vs IgG control rationale, rRNA / snoRNA contamination, fragment-length distribution, and ENCODE-compliance thresholds. Use when assessing whether a CLIP library passed, deciding lenient vs stringent peak thresholds, comparing replicates with IDR rescue and self-consistency ratios, or distinguishing failed IP from over-amplified library.

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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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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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Use this skill when the user asks about driver ergonomics — back/neck/shoulder injury prevention, seat adjustment + lumbar support, entering and exiting cab safely, load handling techniques, vibration reduction, stretching protocols, and how ergonomics affects workers compensation costs in trucking. Reference OSHA + ATA ergonomics research.

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Comprehensive SEO analysis for any website or business type. Full site audits, single-page analysis, technical SEO (crawlability, indexability, Core Web Vitals with INP), schema markup, content quality (E-E-A-T), image optimization, sitemap analysis, and GEO for AI Overviews/ChatGPT/Perplexity. Industry detection for SaaS, e-commerce, local, publishers, agencies. Triggers on: SEO, audit, schema, Core Web Vitals, sitemap, E-E-A-T, AI Overviews, GEO, technical SEO, content quality, page speed.

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。

SE Ranking AI visibility analyst (extension). Tracks AI Share-of-Voice across ChatGPT, Gemini, Perplexity, AI Overviews, and AI Mode in a single query.

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Profound LLM citation tracker (extension). Time-series brand citation rates across ChatGPT, Perplexity, and other LLMs. Pairs with seo-seranking for triangulated AI visibility coverage.

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。

Generative Engine Optimization for AI search engines (ChatGPT, Claude, Perplexity). Use when improving how content is discovered and cited by AI assistants.

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Strip designs to their essence by removing unnecessary complexity. Great design is simple, powerful, and clean. Use when the user asks to simplify, declutter, reduce noise, remove elements, or make a UI cleaner and more focused.

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Cost optimization patterns for LLM API usage — model routing by task complexity, budget tracking, retry logic, and prompt caching.

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Design spec with 98 rules for building CLI tools that AI agents can safely use. Covers structured JSON output, error handling, input contracts, safety guardrails, exit codes, and agent self-description.

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Optimize content for AI search and LLM citations across AI Overviews, ChatGPT, Perplexity, Claude, Gemini, and similar systems. Use when improving AI visibility, answer engine optimization, or citation readiness.

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Complete SEO + GEO (Generative Engine Optimization) system for SaaS companies wanting to rank on both Google and AI search engines (ChatGPT, Perplexity, Gemini, Claude). Use this skill whenever the user asks about SEO strategy, keyword research, content planning, writing SEO-optimized articles, auditing their search performance, creating a content calendar, analyzing competitors, or optimizing for AI search visibility. Trigger on: "seo", "keyword research", "content calendar", "rank on google", "search traffic", "write an article", "blog post", "serp", "backlinks", "competitor analysis", "content cluster", "seo audit", "geo optimization", "ai search", "search console", "organic traffic", "content strategy", "publish article", "seo setup", "ranking", "impressions", "ctr", "meta description", "schema markup", "faq schema". Also trigger when a user wants to set up their SaaS blog SEO from scratch, analyze their current rankings, or create a publishing workflow.

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 chatmode or prompt files and recommend optimal AI models based on task complexity, required capabilities, and cost-efficiency

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 self-serve acquisition and expansion motions. Use when deciding PLG vs sales-led, optimizing activation, driving freemium conversion, building growth equations, or recognizing when product complexity demands human touch. Includes the parallel test where sales-led won 10x on revenue.

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Analyze a screen recording of a manual process and produce targeted, working automation scripts. Extracts frames and audio narration from video files, reconstructs the step-by-step workflow, and proposes automation at multiple complexity levels using tools already installed on the user machine.

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Build leveraged buyout models in Excel — sources & uses, debt schedule, cash sweep, exit multiple, IRR/MOIC sensitivity. Pairs with excel-author. Use for PE screening, sponsor-case valuation, or illustrative LBO in a pitch.

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Simplify cluttered UI by removing unnecessary elements, choices, features, and structural complexity. Use when the problem is too many controls, options, features, or competing elements—not when the structure is sound and the real issue is only visual intensity or lack of personality.

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Route a task by complexity and run the gated Forge pipeline (research → plan → implement → ship). Use when the user runs /forgemaster or wants the full guided feature pipeline.

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。

Structures CLI app layers. Command/handler/service separation, clig.dev principles, exit codes.

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Deploy and configure Tailscale as a WireGuard-based zero trust mesh VPN with identity-aware access controls, ACLs, and exit nodes for secure peer-to-peer connectivity.

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。