「network」の検索結果

Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.

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Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring. Covers the motif-pruning-as-directionality principle, regulon specificity scoring, run-to-run stability, and database/species matching. Use when identifying TF regulons, scoring TF activity per cell, finding master regulators of cell identity, or comparing regulon activity across conditions. For enhancer-driven multiomic GRNs see multiomics-grn; for bulk inference and VIPER protein-activity see grn-inference.

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Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).

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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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Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, DIP). Use when building PPI networks, choosing between physical vs functional vs genetic interactions, signed/directed vs undirected, high-throughput vs curated, picking confidence thresholds, aggregating across resources, or navigating license constraints. Encodes the database decision matrix, STRING v12 channel semantics, OmniPath as meta-database, SIGNOR for signed signaling, and per-resource rate limits.

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Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency safety, and luminance-monotonicity criteria. Covers Crameri scientific colormaps, viridis/cividis/magma, Okabe-Ito categorical, ColorBrewer, and the rainbow/jet critique. Use when choosing palettes for heatmaps, scatter, networks, or any encoding where color carries quantitative or categorical meaning.

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers between conditions, identifying master transcription factor networks, or predicting BET-inhibitor responsiveness.

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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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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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Install, instrument and verify this running web app from the inside (DOM, network, routing, console and framework state) instead of screenshots or guessing. Drives one real flow end to end and returns a verdict with the file:line to fix. Use when the user asks to set up or install Reticle, when a user-facing change needs proving before you call it done, when a test passes but the UI is broken, or when the user types /reticle.

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Verify that a web app change actually works by driving the running app from the inside (DOM, network, routing, console, framework state) instead of screenshots or guessing. Use after any user-facing change, when a fix is claimed but unproven, when a test passes but the UI is broken, or when you need a real verdict rather than "looks right". Also use to install and wire up Reticle in a project that does not have it yet.

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Use when work crosses into Apple's system surfaces rather than your own UI or data — Siri and Shortcuts, widgets, Live Activities, in-app purchase, localization, privacy prompts, alarms, timers, calendar, reminders, contacts, SharePlay, VoIP and CallKit, accessory pairing, weather, Spotlight indexing, background tasks, Background Assets, push, or push on networks with no internet.

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Manages iOS Simulator devices and app tests with xcrun simctl: lifecycle, install/launch, push and location simulation, privacy permissions, deep links, status-bar overrides, screenshots/video, log streaming, app containers, and targetEnvironment(simulator). Use when scripting Simulator workflows, debugging CoreSimulator boot failures, or deciding which hardware, performance, networking, memory-pressure, and security behaviors require a physical device.

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Debug iOS apps and profile performance using LLDB, the interactive Memory Graph Debugger, and Instruments. Use for crashes, retain-cycle inspection, hangs, build failures, and generic CPU, memory, energy, or network profiling. Use ios-memgraph-analysis for .memgraph capture, leaks CLI ownership paths, or persistent heap growth; use ios-ettrace-performance for ETTrace capture and JSON.

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Measure ad effectiveness with privacy-preserving attribution using AdAttributionKit. Use when registering ad impressions, handling attribution postbacks, updating conversion values, implementing re-engagement attribution, configuring publisher or advertiser apps, or replacing SKAdNetwork with AdAttributionKit for ad measurement.

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Implement, review, or improve CloudKit and iCloud sync in iOS/macOS apps. Use when working with CKContainer, CKRecord, CKQuery, CKSubscription, CKSyncEngine, CKShare, NSUbiquitousKeyValueStore, or iCloud Drive file coordination; when syncing SwiftData models via ModelConfiguration with cloudKitDatabase; when handling CKError codes for conflict resolution, network failures, or quota limits; or when checking iCloud account status before performing sync operations.

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This skill should be used when user asks to "deploy to Hetzner", "create Hetzner server", "manage Hetzner Cloud", "hcloud CLI", or works with Hetzner Cloud infrastructure including servers, networks, firewalls, load balancers, DNS zones, and volumes.

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Discover and choose Cloudflare products for apps, APIs, AI agents, storage, networking, and security. Use for architecture and product selection, including when the user describes a need without naming a Cloudflare product; then find the relevant skill or documentation.

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Reverse-engineer a website's internal API by recording browser traffic into a HAR file, then generate a standalone client or CLI that calls the endpoints directly, with no browser needed after the first recording. Use when asked to "derive a client", "build a CLI for <site>", "reverse engineer this site's API", "record network requests", "turn this site into an API", or when the same site will be automated repeatedly and direct HTTP calls would beat driving the browser every time.

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Set up and verify a connection to an NI USRP radio (USRP E320, N300, N310, N320, N321, X300, X310, or X410) using Wireless Testbench. Use when connecting a USRP for the first time, configuring radio hardware, troubleshooting connection failures, or verifying a radio setup. Covers host inspection (OS, NIC type/speed/MTU), device discovery (findsdru, probesdru), UHD version checking, programmatic radio configuration, and basebandTransceiver verification. Also use when the user mentions USRP setup, radio not found, connection errors, dropped samples, or network configuration for SDR hardware.

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Integrate antennas into RF systems using MATLAB Antenna Toolbox and RF Toolbox. Covers impedance matching network design (L/Pi/Tee topologies, evaluation parameters, Richards transformation), measured antenna creation (E-field, directivity-only, EmbeddedE, ffsReader import), RF propagation and site planning (txsite/rxsite, coverage, SINR, ray tracing, link budget), and SAR estimation (birdcage+Phantom, conformalArray+Custom3D, direct EHfields). Use when the user wants to match an antenna, create a measuredAntenna, compute coverage or signal strength, perform ray tracing, or estimate SAR.

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Discover OPC UA servers, connect MATLAB clients, and browse/navigate server nodes using opcuaserverinfo, the Local Discovery Service (LDS), opcua, connect, setSecurityModel, certificate-trust functions, findNodeById, opcuanode, and Namespace/Children traversal. Use when finding OPC UA servers on the network, querying endpoints and security policies, connecting to a server, authenticating with username/password or certificates, configuring security modes, handling certificate-trust or hostname-mismatch errors, troubleshooting failed connections or empty discovery, inspecting an OPC UA certificate (.der/.pem), browsing an address space, finding nodes by name or NodeId, navigating node hierarchies, invoking method nodes, or batch-processing large namespaces. Trigger on: opcuaserverinfo, LDS, opcua, opc.ua.Client, setSecurityModel, opc.ua.trustServerCertificate, OPC UA certificate, findNodeById, opcuanode, browse OPC UA, find node, OPC UA namespace, OPC UA method node, Industrial Communication Toolbox.

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Discover MATLAB Parallel Computing Toolbox clusters on the network and in the cloud, and manage their profiles — list, inspect, import, export, set default, validate, and delete. Use whenever the user asks what parallel computing resources, clusters, or cluster profiles they have or can use — e.g. "what parallel resources do I have", "show my cluster profiles", "list clusters", "what clusters can I run on", "where can I submit jobs" — and for any work with parcluster, parallel.listProfiles, parallel.defaultProfile, MJS / Generic / HPC Server / MJSComputeCloud clusters, .mlsettings files, or profile validation. Does NOT cover job submission, parpool, or parfor.

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