'normalization' 검색 결과

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) with SES scaling, 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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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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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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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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Design relational database schemas (and choose when to go NoSQL) that stay maintainable and fast. Use this skill whenever the user mentions tables, DDL, entities and relationships, normalization (1NF/2NF/3NF), primary and foreign keys, UUID vs bigint IDs, indexes (B-tree, composite, covering, partial), EXPLAIN, constraints (CHECK, UNIQUE, exclusion), transactions and isolation levels, migrations (Alembic, Prisma, Flyway, expand-contract, backfilling), or SQL vs NoSQL (MongoDB, DynamoDB, Cassandra, graph databases). Also trigger for "design the database", "model this domain", "which database should I use", or writing ORM models and migration files for PostgreSQL, MySQL, SQLite, or SQL Server.

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Normalizes company names, industries, domains, locations, and descriptions. Use when the user provides company records and wants consistent canonical fields with confidence and unresolved items flagged.

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Converts inconsistent job titles into standardized role, department, and seniority labels. Use when the user provides records with free-text titles and wants consistent role family, department, and seniority fields.

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Use when designing a new relational schema or auditing an existing one — normalization, keys and constraints, indexing strategy, and spotting modeling problems before they reach production.

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Correlate events across multiple log files from different sources, systems, or time periods. Build unified timelines, identify causal relationships between events, and highlight anomalies that span multiple data sources. Supports timezone normalization and gap detection. Use when analyzing logs from multiple systems (frontend, backend, database, infrastructure), investigating distributed system failures, or building event timelines across services. Triggers: "correlate these logs", "build timeline from multiple logs", "cross-system analysis", "find related events across logs", "multi-source log analysis", "distributed trace analysis"

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Builds automated threat intelligence feed integration pipelines connecting STIX/TAXII feeds, open-source threat intel, and commercial TI platforms into SIEM and security tools for real-time IOC matching and alerting. Use when SOC teams need to operationalize threat intelligence by automating feed ingestion, normalization, scoring, and distribution to detection systems.

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Knowledge base from the NASA Cost Estimating Handbook (CEH) v4.0. Use for NASA's 12-step, three-part cost estimating process (Project Definition, Cost Methodology, Cost Estimate); the WBS, CADRe, and ONCE data backbone; estimating methodologies (analogy, parametric/CER, engineering build-up, EVM, Delphi); ground rules and assumptions, data normalization and inflation (BY/CY/RY); the point-estimate-to-S-curve cost-risk chain and Unallocated Future Expense (UFE) reserves; Joint Cost and Schedule Confidence Level (JCL) analysis via probabilistic cost-loaded schedules; decision-support analyses (sensitivity, trade studies, make/lease-vs-buy, affordability, CAIV); and economic analysis (discounting, NPV, OMB Circular A-94). The cost-estimating complement to NASA's SE and risk packs. Does NOT reproduce the handbook's tool-specific procedures, worked examples, or appendix-depth methods (it names the appendices), nor cover full DoD/GAO cost guides, schedule construction, or formal risk management beyond the cost interface.

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MSBuild property definition patterns: conditional defaults, composition/concatenation, path normalization, trailing slash handling, TFM detection helpers, and property evaluation order. Only activate in MSBuild/.NET build context. USE FOR: diagnosing and fixing MSBuild property definition issues in .props or .csproj files, reviewing and fixing shared property configuration anti-patterns, fixing DefineConstants or NoWarn being overwritten instead of appended, fixing unconditional property assignments that prevent project-level overrides, fixing unquoted conditions that fail when properties are empty, fixing hardcoded paths that break cross-platform builds, setting property defaults that can be overridden, understanding property evaluation order and last-write-wins semantics. DO NOT USE FOR: props vs targets placement (use directory-build-organization), item operations (use item-management), target structure (use target-authoring), general anti-patterns (use msbuild-antipatterns), non-MSBuild build systems.

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Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis.

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Enforces error handling standards: silent error prohibition, custom error class hierarchy (AppError base with category never-fallback / transient / permanent, cause preservation, ValidationError / UnauthorizedError / UpstreamError etc. — canonical definitions in ERRORS.md), external-boundary normalization (normalizeExternalError), Result pattern (Result.ok/Result.fail), proper try-catch with error type checking, structured error logging with a single Logger contract, fallback prohibition categories (isNeverFallback), and HTTP status code mapping. Use when implementing error handling, reviewing catch blocks, or designing error responses.

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Design database schemas with normalization, relationships, and constraints. Use when creating new database schemas, designing tables, or planning data models for any database paradigm.

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How to identify and test for account takeover vulnerabilities in web applications. Use this skill whenever the user mentions account takeover, authentication bypass, password reset attacks, email verification bypass, session hijacking, or any technique to compromise user accounts. This includes testing authorization issues, unicode normalization attacks, reset token reuse, CORS/CSRF/XSS exploitation, cookie manipulation, and OAuth vulnerabilities.

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Builds automated threat intelligence feed integration pipelines connecting STIX/TAXII feeds, open-source threat intel, and commercial TI platforms into SIEM and security tools for real-time IOC matching and alerting. Use when SOC teams need to operationalize threat intelligence by automating feed ingestion, normalization, scoring, and distribution to detection systems.

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Design database schemas — tables, relationships, indexes, constraints, and ORM setup. Covers relational design, normalization, and common patterns.

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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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End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation. Use when analyzing single-cell RNA-seq data.

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End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with limma (default) or MSstats for complex feature-level designs. Use when processing mass spectrometry proteomics.

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Orchestrates the untargeted LC-MS metabolomics pipeline end-to-end (xcms 4.x feature extraction, QC/drift/normalization, confidence-stratified annotation, permutation-validated statistics, background-aware pathway mapping), naming what each stage decides and where it silently fails. Use when running a full LC-MS metabolomics study from raw mzML to enriched pathways and needing the honest handoffs between stages. Each stage defers to its component skill for parameters and traps; for stable-isotope flux (a separate branch, not this untargeted flow) see metabolomics/isotope-tracing.

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Orchestrates the end-to-end germline short-variant pipeline from FASTQ to a filtered, normalized, benchmarked VCF, chaining QC/trim, BWA-MEM2 alignment, duplicate marking, optional BQSR, calling (bcftools/GATK HaplotypeCaller/DeepVariant/DRAGEN), normalization, site+genotype filtering, annotation, and hap.py/vcfeval benchmarking. Use when deciding the pipeline-wide reference-genome commitment (GRCh38 analysis set vs T2T, ALT/decoy handling), sequencing the steps in the defensible order (normalize BEFORE annotate, filter site- then genotype-level), choosing the calling engine and single-sample vs cohort joint-calling, picking a filtering strategy by cohort size, or benchmarking stratified within GIAB confident regions. Hands off mechanism to the variant-calling and read-alignment component skills; not a re-teach of any single step.

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Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautomer canonicalization, stereochemistry standardization, mixture handling, and isotope normalization. Explicitly compares ChEMBL pipeline, canSARchem, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compound collections, or building canonical compound registries.

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