'chips' 검색 결과

Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract, SES), k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CTCF-only/DNase-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract, SES), k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.

Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Analyzes UEFI bootkit persistence mechanisms including firmware implants in SPI flash, EFI System Partition (ESP) modifications, Secure Boot bypass techniques, and UEFI variable manipulation. Covers detection of known bootkit families (BlackLotus, LoJax, MosaicRegressor, MoonBounce, CosmicStrand), ESP partition forensic inspection, chipsec-based firmware integrity verification, and Secure Boot configuration auditing. Activates for requests involving UEFI malware analysis, firmware persistence investigation, boot chain integrity verification, or Secure Boot bypass detection.

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Prototype a single-page website for SaaS, documentation, or knowledge products. Use warm off-white backgrounds, serif headings, fine dividers, generous spacing, and subtle motion to create a restrained layout with features and a signup or pricing section.

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• Prototype a SaaS marketing page
• Explore a documentation page design
• Build an introduction page for a knowledge product

Create breadboard layout diagrams with HTML5 Canvas to show electronic components and wire connections. Use the skill for LED circuits, 555 timers, and 6502 computer projects, with component references, labels, and color-coded wiring.

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• Plan component placement for an LED circuit
• Draw a breadboard layout for a 555 timer
• Visualize wiring for a 6502 computer

Investigate malware hidden in boot records, UEFI firmware, or the operating system’s core. The skill guides evidence collection, boot integrity checks, firmware and memory analysis, and reporting of persistence mechanisms and remediation steps when compromise survives an OS reinstall.

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• Investigating infections that survive an OS reinstall
• Examining unexplained Secure Boot integrity violations
• Finding hidden processes and suspicious kernel drivers

Create a magazine-inspired web prototype with a warm monochrome background, generous whitespace, and subtle motion. Combine serif headings, simple sans-serif body text, monospaced metadata, fine borders, and softly styled chips for a restrained layout.

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• Explore a magazine-inspired web layout
• Prototype a page with generous whitespace
• Try typography with subtle visual accents

Assess WPS, a router feature for easy Wi-Fi setup, for weaknesses in PIN authentication. The skill covers device discovery, offline and online testing, lockout behavior, and how a recovered PIN can expose the network password.

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• Assessing WPS exposure on home and small-office routers
• Comparing offline and online PIN testing methods
• Reviewing PIN lockouts and push-button pairing behavior

Plan or run quality checks and peak calling, which identifies enriched genomic regions, for ChIP-seq, CUT&RUN, and CUT&Tag. The workflow accounts for controls and replicates and prepares signal tracks, quality reports, and differential binding designs.

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• Check data quality and enrichment signals
• Choose narrow or broad peaks for the biological target
• Create bigWig tracks and quality dashboards

Create and edit Google Docs while preserving requested structure, formatting, tabs, and tables. Adapt templates using current source information, update links and smart chips, and check that the finished document covers the requested content.

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• Create a document from a Google Docs template
• Update text and tables while preserving formatting
• Adapt a past project document for new work

Build continuous scrolling rows for logos, testimonials, screenshots, or short tags. The skill explains how to duplicate content, stabilize item widths, soften edges, and accommodate people who prefer reduced motion.

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• Build a continuously scrolling logo row
• Loop screenshots or testimonials
• Add a moving row of tags or feature chips

Add animated liquid-metal borders to React buttons, cards, tabs, and other surfaces using metal-fx. The skill covers visual tuning, linking effects to interaction states, preserving keyboard access, and providing static borders when animation or WebGL is unavailable.

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• Highlighting selected tabs and filters
• Adding metallic borders to primary buttons
• Tuning card borders, glow, and corner radius

Build ice and frost visual effects in Three.js using reusable modules. Combine branching frost growth, refractive ice spikes, cracks and settling fragments, freezing mist, and swirling snow into a coordinated sequence demonstrated on a snowy ground.

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• Animate frost spreading across the ground
• Create erupting ice spikes that crack and shatter
• Combine freezing mist with a swirling blizzard

The reference presentation-tool contract, covering server-side enrichment, suggestion chips, the event stream, progressive rendering, both roles' built-in components, and adding a vertical component. Load when building or reviewing how a commerce agent's output reaches a frontend.

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De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.

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Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.

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ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files. Use when calling peaks from ChIP-seq alignments.

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Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between conditions.

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ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.

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Render pixel-accurate ChatGPT mobile (iOS) screen mockups in light mode from a thread JSON. Supports user text bubbles, user image attachments, assistant markdown prose, citation chips, the OpenAI spiral logo, the Apps-SDK GPT chip in the composer, and three header styles (model-tag, plain title, "Get Plus"). Fixed 9:16 viewport. Outputs HTML + PNG.

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Render a 'photo-grid promo card' video from a config — a real-DOM card with a FIXED header/footer and a CONTINUOUSLY SCROLLING 2-row grid of MIXED tiles (video clips, product/lifestyle stills, big-serif %-OFF, dark promo-code or CTA) + feature chips, frame-stepped via Playwright with real-time <video> playback and encoded with FFmpeg — deterministic assembly, FREE (the clips + music come from create-video-fal + create-music-elevenlabs), text stays pixel-crisp. Use for the photo-grid-promo-card format.

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