「chips」の検索結果

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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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.

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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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Editorial-minimalist web prototype. Warm monochrome canvas, serif display + grotesque body, 1px hairline borders, muted pastel chips, generous macro-whitespace, ambient micro-motion. Distilled from Leonxlnx/taste-skill `minimalist-skill`.

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Designs custom laboratory hardware as parametric build123d models and exports fabrication artifacts as STEP, STL, and DXF files - microfluidic chips and molds, optomechanical mounts and breadboard adapters, cuvette and microplate holders, tube racks, animal-behavior rigs, and 3D-printed instrument fixtures. Use when a research task needs a physical part that must mate with standardized labware, an optical table, a cage system, or a printer, CNC, or laser process.

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Generate breadboard circuit mockups and visual diagrams using HTML5 Canvas drawing techniques. Use when asked to create circuit layouts, visualize electronic component placements, draw breadboard diagrams, mockup 6502 builds, generate retro computer schematics, or design vintage electronics projects. Supports 555 timers, W65C02S microprocessors, 28C256 EEPROMs, W65C22 VIA chips, 7400-series logic gates, LEDs, resistors, capacitors, switches, buttons, crystals, and wires.

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WPS (Wi-Fi Protected Setup) PIN attack methodology — Pixie Dust offline attack against vulnerable chipsets (Ralink, Realtek, Broadcom, MediaTek), online PIN brute-force with reaver/bully, lockout handling, time-of-day evasion, WPS push-button vulnerability windows, and PIN-to-PSK derivation. Use when a target SOHO router exposes WPS — common on consumer ISP gear, often left enabled by default even when WPS attacks have been known for over a decade.

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Add and tune animated liquid-metal WebGL borders with the React `metal-fx` package. Use when buttons, icon controls, chips, tabs, cards, or selected surfaces need a metallic active, selected, hover, focus, or premium border; when implementing the MetalFx component from metal.jakubantalik.com; or when troubleshooting its presets, themes, strength, glow, reflections, sizing, radius, animation, accessibility, SSR, or performance.

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Build the effects of an ice and frost skill as one visual language in Three.js. Frost that grows like real frost, not a painted fern: a dendritic tree grown on the CPU from a seed point, stems racing outward with barbs and sub-barbs that compete for space in one time-ordered queue, side branches leaned toward their tips, baked into a distance field so the shader draws hairline feathers growing out from the seed with a bright tip, rime, crystal glints and a contact shadow. Faceted ice spikes built from half-spaces and ray-traced against their own planes (Snell, Fresnel, total internal reflection, Beer-Lambert blue, trapped bubbles, a fracture network, frosted edges) that erupt along the frost line, crack along visible planes and shatter into convex pieces that tumble, land on a face and rest, with snow lumps and ice chips settled into the crust. A low freezing mist marched as wind-stretched banks that churn in place and part around the ice, a blizzard column of powder on helical strands with a fibrous veil, glinting diamond dust, and a scanned snow floor with dunes, broken crust, a raking moon with self-shadow and two populations of glints. Use for ice or frost skills, frost novas, ice spikes or walls, glacial eruptions, shattering ice, blizzards, snow devils, freezing mist, frozen ground, "ice and frost", "frost creep", "ice shards", "realistic ice" or "skill effects only". Includes two reusable modules and a five-beat demo on a scanned CC0 snow floor with a failure-mode switch.

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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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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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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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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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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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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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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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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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