「graph」の検索結果

End-to-end clinical trial analysis workflow from CDISC SDTM/ADaM loading through ICH E9(R1) estimand-driven primary analysis to CONSORT 2025 regulatory-compliant reporting. Covers data preparation, FDA 2023 marginal vs conditional logistic regression, categorical tests with Boschloo, modern HTE/subgroup methods, missing-data sensitivity (MMRM, reference-based MI, Permutt tipping point), graphical multiplicity (Bretz-Maurer), survival analysis (Cox/RMST/competing risks) when applicable, and Table 1. Use when performing a complete analysis of clinical trial data.

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Add custom local tools to ToolUniverse alongside the 1000+ built-in tools. Covers JSON-config tools (simplest, no code), Python class tools (REST/SOAP/GraphQL APIs, computational logic), and best-practices for return schemas. Use for wrapping new APIs, adding domain-specific computations, or contributing tools to the registry.

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Drug safety and adverse event analysis — FAERS spontaneous-report mining, FDA black-box warnings, signal detection (PRR, ROR, IC), risk factors by demographic/comorbidity, and label change tracking. Use for post-market safety surveillance, AE signal investigation, drug-AE association strength scoring, and pharmacovigilance reports.

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Guidance for distinctive, intentional visual design when building new UI or reshaping an existing one. Helps with aesthetic direction, typography, and making choices that don't read as templated defaults.

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Apple's approach to interface design and fluid, physical motion, translated for the web. Use when building or reviewing gesture-driven UI, spring animations, drag/swipe/sheet interactions, momentum and interruptible transitions, translucent materials and depth, typography (optical sizing, tracking, leading), reduced-motion, or the design foundations (feedback, spatial consistency, restraint) behind Apple-style interfaces.

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Implement construction graphs, machine lifecycle, power, parts, upgrades, examination, and machine UI.

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Define or review a visual system, DESIGN.md, or redesign direction. Use for typography, layout, color, motion, and interaction design decisions.

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Generate an Open Graph social sharing card with dynamic title, description, and branding.

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Generate a branded Open Graph image with a generative wave background, logo, and tagline.

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Imports a custom RoadRunner map (FBX geometry + XODR OpenDRIVE) into a CARLA source build as a drivable map — reads the map from the directory the user names, runs CARLA's Import.py to cook the level, Traffic Manager graph and (standard maps only) pedestrian navmesh, and verifies it loads on a server. Handles both standard maps and large tiled maps; large maps get no navmesh, matching upstream CARLA. Use when the user asks to "import a map into CARLA", "add a custom/RoadRunner map", "ingest an FBX+XODR map", "make import", bring in a "large/tiled map", or fix missing walkers / a missing pedestrian navmesh.

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Send and receive cryptographically signed messages between AI agents using the Agent Messaging Protocol (AMP). Use when the user asks to "send a message to an agent", "check agent inbox", "message another agent", "reply to a message", "notify an agent", or any inter-agent communication task.

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Sous-agent spécialisé dans les appels API REST/GraphQL avec retry, auth et transformation de données. Se déclenche avec "sous-agent API", "API caller agent", "agent qui appelle une API", "REST agent", "HTTP agent", "API integration subagent", "external API agent".

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Use proactively for authorization with ActionPolicy. Creates policies, scopes, and integrates with GraphQL/ActionCable. Preferred over Pundit for composable, cacheable authorization.

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AAWP (AI Agent Wallet Protocol) — the only crypto wallet protocol built exclusively for AI Agents on EVM-compatible blockchains and Solana. Not for humans. The signer is the AI Agent itself, cryptographically bound at wallet creation. Supports wallet lifecycle management, token transfers, DEX swaps, cross-chain bridging, Solana native trading (Pump.fun SDK + Jupiter), token launches, DCA automation, and price alerts.

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Expert in groups, rings, fields, and algebraic structures with applications to cryptography and number theory

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Use when you need to apply Java secure coding best practices — including validating untrusted inputs, defending against injection attacks with parameterized queries, minimizing attack surface via least privilege, applying strong cryptographic algorithms, handling exceptions securely without exposing sensitive data, managing secrets at runtime, avoiding unsafe deserialization, and encoding output to prevent XSS. This should trigger for requests such as Review Java code for secure coding. Part of cursor-rules-java project

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Scan, structure, validate, and submit your project to the Next Level Builders Directory (https://nextlevelbuilder.io) with 17 rich blocks, cryptographic content hashing, Polar payment handling, and automated moderation queueing.

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Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (windowed depth, cumulative distribution, --quantize callable BEDs), bedtools genomecov/coverage (bedGraph tracks, per-target stats), samtools depth/coverage (per-base depth, per-contig depth+breadth). Covers the breadth-vs-mean distinction, the cumulative-coverage curve, evenness (CV/Fano/fold-80/Gini), what each tool silently counts (duplicates, secondary/supplementary, MAPQ, read span vs fragment, mate-overlap), the samtools-depth 8000-cap version trap, and the bedtools coverage -a/-b orientation flip. Use when assessing sequencing adequacy, building coverage tracks, computing breadth at a depth threshold, defining callable regions, or QCing target-capture uniformity.

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Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.

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Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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Assign cell types from marker expression in IMC/MIBI data using clustering (PhenoGraph/FlowSOM/Leiden/Pixie), marker-based probabilistic classifiers (Astir), or image-context CNNs (CellSighter), covering the double-positive segmentation artifact, lineage-vs-state markers, the two spillover types, and why a "cell type" in imaging is conditioned on a segmentation guess. Use when phenotyping segmented IMC cells, choosing clustering vs classification, diagnosing implausible double-positive populations, separating lineage from functional markers, or transferring labels across a cohort.

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Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical models. Covers signed-network choice, soft-threshold selection, module preservation, and the marginal-vs-partial-correlation distinction. Use when finding co-expression modules, identifying hub genes, relating gene networks to clinical or experimental traits, or building single-cell co-expression networks. For directed TF-target inference see scenic-regulons and grn-inference; for condition rewiring see differential-networks.

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Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requires imputed genotypes), OutFLANK with trimmed FST null, pcadapt, gradient forests (Ellis-Smith-Pitcher 2012, NOT mis-cited Ellis-Manel), Capblancq & Forester 2021 RDA Swiss-army-knife, genomic-offset prediction with Lind & Lotterhos 2025 three-regime caveat, Lotterhos-Whitlock sampling optima, Wang & Bradburd 2014 IBD vs IBE, and Circuitscape + ResistanceGA. Use when identifying adaptive loci across gradients, choosing K for LFMM2, deciding among GEA methods, predicting maladaptation with the novel-environment caveat, distinguishing IBD vs IBE, or optimizing sampling design.

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