'matrix' 검색 결과

Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.

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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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Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.

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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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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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Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.

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Build UpSet plots to visualize set intersections beyond 4 sets (where Venn fails) using ComplexUpset (modern, ggplot2-grammar) or the unmaintained UpSetR, with explicit cardinality vs degree sorting, attribute panels, and query highlighting. Use when comparing overlap across many gene sets, peak sets, variant lists, or any set membership matrix where Venn diagrams become illegible.

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Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles results against MTAG multi-trait analysis. Handles sample overlap via the LDSC sampling-covariance matrix, identifies and resolves Heywood cases, and verifies model fit with CFI / RMSEA. Use when modeling latent genetic architecture across correlated traits, running multivariate GWAS on a shared factor, distinguishing factor-mediated from trait-specific SNP effects, or comparing GenomicSEM common-factor results against MTAG when both depend on accurate sampling covariance.

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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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Validates versioned permission requests against a grant scope and records comparison evidence. Activate on 'validate permissions', 'permission check', 'inheritance validation', 'permission matrix', 'security validation'. NOT for runtime enforcement (use dag-scope-enforcer) or isolation management (use dag-isolation-manager).

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Own whether a multi-document product-architecture binder is internally consistent, complete against its stated customer/contingency/architecture coverage, and honest about which older product ambitions it has absorbed, superseded, deferred, contradicted, orphaned, or rejected. Use when running a binder Architect of Record pass, before an implementation chain cites a binder chapter as ready, when a proof-gate owner is missing, or when reconciling the binder against the older ambition corpus (website, plans, examples, ADRs). NOT for auditing a single Claude Skill bundle's structure or frontmatter (use skill-hygiene), rendering a single-PM accept/reject verdict on one finished deliverable (use port-daddy-user-surrogate-pm-review), or sequencing/stewarding a roadmap's sidequests once a gap or operator decision has been surfaced (use legible-roadmap-with-sidequests).

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Design or review a declared control-command profile and its verb/backend lifecycle matrix. Distinguish policy denial, unsupported capability, delivery acknowledgement, independently observed effect, and unknown outcome; bind authorization to principal, target, scope, current policy, expiry, and fencing epoch. NOT for claiming runtime correctness, proving an adapter from declarations, or approving a control-panel button without independent runtime evidence.

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Evaluate strategic options by NPV vs ease of implementation. Use for project prioritization, resource allocation, and strategic decision making.

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Framework-directable information security risk assessment. Identifies threats, evaluates likelihood/impact via a 3x3 matrix, maps findings to any compliance framework, and recommends risk treatment options with prioritization guidance.

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Define roles and responsibilities using RACI matrix. Use for process improvement, organizational design, project management, and change initiatives.

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Identify and prioritize risks by impact and controllability. Use for risk management, project planning, and strategic decision support.

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Manage the Matrix/Virgo-Core Proxmox VE cluster (nodes Foxtrot, Golf, Hotel - MINISFORUM MS-A2 with AMD Ryzen 9 9955HX). Covers VM provisioning, VLAN networking, CEPH storage, and automation via Python (proxmoxer), Ansible (community.general.proxmox), and Terraform (Telmate/proxmox).

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CI/CD pipeline patterns with GitHub Actions, release automation, and testing strategies. Use for: github actions, workflow, CI, CD, pipeline, deploy, release, semantic release, changesets, goreleaser, matrix, cache, secrets, environment, artifact, reusable workflow, composite action.

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Chooses inter-service protocols. REST vs gRPC vs SignalR vs SSE decision matrix, tradeoffs.

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Composes GitHub Actions workflows. Reusable workflows, composite actions, matrix, caching.

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Chooses a data access approach. EF Core vs Dapper vs ADO.NET decision matrix, tradeoffs.

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Releases CLI tools. GitHub Actions build matrix, artifact staging, Releases, checksums.

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Chooses CLI output format. AOT vs framework-dependent, RID matrix, single-file, dotnet tool.

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This skill outlines methodologies for performing authorized penetration testing against AWS, Azure, and GCP cloud environments. It covers understanding the shared responsibility model for testing scope, leveraging cloud-specific attack tools like Pacu and ScoutSuite, exploiting IAM misconfigurations, testing for SSRF to cloud metadata services, and reporting findings aligned to MITRE ATT&CK Cloud matrix.

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