「interaction」の検索結果

Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound, inhomogeneous Ripley's K, cellular-neighborhood discovery, graph-construction (contact vs proximity), and edge effects. Use when testing whether cell types co-locate, choosing a spatial null, building a neighbor graph, discovering tissue niches, or deciding whether a spatial pattern is real or a density/segmentation artifact.

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Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-bias-aware differential via its bam_ip/bam_input control + bam_treated_ip/bam_treated_input treatment arms), QNB beta-binomial, MeTDiff HMM, and RADAR, plus the paired-symmetric edgeR/DESeq2-on-peak-counts route when batch/lot covariates need fixed-effect handling that exomePeak2's API does not accept. Covers paired vs unpaired vs interaction designs, batch confounding and per-lot meta-analysis, the stoichiometry-vs-expression-vs-IP-efficiency confound, and effect-size filtering against under-powered N=2 designs. Use when comparing m6A across two or more conditions, choosing between exomePeak2/QNB/RADAR/MeTDiff for a design, handling batch confounding when exomePeak2's API is too rigid, distinguishing real hyper/hypo-methylation from expression shifts, applying effect-size thresholds, or planning orthogonal stoichiometry validation (GLORI/SAC-seq/m6Anet mod_ratio).

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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.

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Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE DESeq), LRT reduced-model rules, the interaction-term resultsNames trap, continuous-covariate scaling and splines, repeated measures via duplicateCorrelation or dream, high-cardinality categorical pseudo-singular designs, sample swap detection via XIST/RPS4Y1 expression and somalier/NGSCheckMate genotypes, SABV (sex-as-biological-variable) mandate, Simpson's-paradox collapsing of technical replicates, and the `~ 0 + group` parameterization for clean contrasts. Use when building a design matrix, troubleshooting reversed fold-change direction, encoding paired or repeated-measures designs, detecting sample swaps, deciding sex-as-covariate, or aggregating technical replicates.

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Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indicator species (indicspecies IndVal.g group-equalized), PERMANOVA paired MANDATORILY with PERMDISP (Anderson & Walsh 2013; dispersion confounds centroid tests), Joint Species Distribution Models (HMSC, sjSDM, gjam) with explicit rejection of "residual covariance equals biotic interaction", phylogenetic community ecology (SES_MPD/MNTD), trait-environment via RLQ + fourth-corner with corrected modeltype=6 (Dray 2014), bipartite network metrics (NODF, modularity) with curveball null (Strona 2014), and Mantel-test replacements (dbRDA, GDM) for spatial data. Use when testing how environmental gradients structure communities, identifying habitat indicator taxa, partitioning variance among predictors, deciding whether PERMANOVA significance is location vs dispersion, picking among HMSC/sjSDM/gjam, or replacing Mantel tests for landscape data.

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Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA targets from indirect, integrating CLIP-derived target maps with TargetScan / miRDB / DIANA predictions, applying canonical 7mer-8mer seed matching with 3' UTR context, or recovering miRNA-mRNA chimeras at scale.

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Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants), Aldy, Stargazer; applies Caudle 2020 activity-score translation. Use when implementing pharmacogenomic-guided prescribing, applying CPIC vs DPWG guidance, screening HLA risk alleles for ICI / antiepileptics / abacavir, or interpreting compound TPMT+NUDT15 thiopurine risk.

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Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible.

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Use when making visual or interaction design decisions for an Apple app — HIG patterns, Liquid Glass, SF Symbols, typography, app entry-point and auth-flow structure.

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Build iOS augmented reality and 3D experiences with RealityKit and ARKit. Use when adding RealityView content, loading entities or USDZ models, anchoring objects to planes or world positions, distinguishing entity hit tests from ARKit real-world raycasts, handling AR camera availability, world tracking, scene updates, or RealityKit entity gestures and interactions.

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Builds multiplayer spatial board games using TabletopKit on visionOS. Use when creating tabletop game experiences with boards, pieces, cards, or dice; managing seats, turns, equipment state, TabletopAction flows, or TabletopInteraction delegates; synchronizing gameplay through FaceTime Group Activities; rendering with RealityKit; or implementing snapping, tosses, and physics on a virtual table surface.

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Access Core Motion accelerometer, gyroscope, magnetometer, device-motion, pedometer, activity-recognition, altitude, headphone motion, batched high-frequency workout motion, and water-submersion/depth data. Use when reading device sensors, counting steps, detecting walking/running/driving/cycling, tracking altitude, building motion interactions, handling AirPods head tracking, or implementing watchOS dive/depth features.

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Implements keyboard, directional, and scene-level focus behavior across SwiftUI and UIKit. Use when managing @FocusState, defaultFocus, focused values, focusable interactions, focus sections, tvOS geometric focus and Siri Remote navigation, watchOS Digital Crown input, visionOS connected-device focus versus gaze hover/input targets, macOS key view loop and Full Keyboard Access, focus restoration after presentation changes, custom focus routing with UIFocusGuide, or debugging focus with UIFocusDebugger.

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Audit, diagnose, or optimize website loading and interaction performance, Core Web Vitals, and Lighthouse performance scores.

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Audit, diagnose, or optimize website loading and interaction performance, Core Web Vitals, and Lighthouse performance scores.

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Exhaustively extract UX patterns from a reference web app. Walks every screen, captures screenshots of every state, records interaction patterns, copy verbatim, keyboard shortcuts, responsive treatments, motion, and empty/error/loading states. Produces a reusable pattern library that other audits can compare against. The inverse of ux-audit — asks 'what is the bar?' rather than 'does this match the bar?'. Trigger with 'learn from X', 'extract patterns from X', 'study X's UX', 'reverse engineer the UX of X', 'build a pattern library from X'.

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Review a web app or page for visual design quality — layout, typography, spacing, colour, hierarchy, consistency, interaction patterns, and responsive behaviour. Not a UX audit (that checks usability) — this checks whether it looks professional and polished. Produces a design findings report with screenshots. Triggers: 'design review', 'does this look good', 'review the design', 'check the layout', 'is this polished', 'visual review', 'design audit', 'make it look better', 'it looks off'.

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Walk through a live web app AS a real user to find usability + behavioural bugs that static reviews miss. REQUIRES proof of interaction (typing, clicking, sending, observing) before any verdict — a sweep that didn't interact terminates with verdict 'Incomplete'. Walks threads, exercises every element, runs the multi-pane stress matrix, visual polish sweep, component perfection checklist, automated a11y (axe-core), pragmatic performance budget (LCP/CLS/INP), scenario battery (11 scenarios), and stress recipes including the real-flavour data battery. Hard gates: console errors/warnings = 0, network 5xx = 0, layout collapse = 0, axe Critical/Serious = 0, perf budget green. Audit-the-audit meta-check rejects rushed reports. Each finding has reproduction steps, evidence path, and suspected code location. Trigger with 'ux audit', 'walkthrough', 'qa sweep', 'audit the app', 'dogfood this', 'check all pages', 'find what's broken', 'stress the UI'.

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Browser automation with persistent named pages via the dev-browser CLI. Use when users ask to navigate websites, fill forms, take screenshots, extract web data, test web apps, log into sites, or automate browser workflows. Trigger phrases include "go to [url]", "click on", "fill out the form", "take a screenshot", "scrape", "automate", "test the website", "log into", "open the browser", or any browser interaction request.

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Lightweight 3D effects for decorative elements and micro-interactions using Zdog, Vanta.js, and Vanilla-Tilt.js. Use this skill when adding pseudo-3D illustrations, animated backgrounds, parallax tilt effects, decorative 3D elements, or subtle depth effects without heavy frameworks. Triggers on tasks involving Zdog pseudo-3D, Vanta.js backgrounds, Vanilla-Tilt parallax, card tilt effects, hero section animations, or lightweight landing page visuals. Ideal for performance-focused designs.

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After Effects animation rendering for web and React applications. Use this skill when implementing Lottie animations, JSON vector animations, interactive animated icons, micro-interactions, or loading animations. Triggers on tasks involving Lottie, lottie-web, lottie-react, dotLottie, After Effects JSON export, bodymovin, animated SVG alternatives, or designer-created animations. Complements GSAP ScrollTrigger and Framer Motion for scroll-driven and interactive animations.

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