「normalization」の検索結果

Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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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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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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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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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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Generate driving scenes, scenarios, road surfaces, and 3D content from scenariobuilder.* sensor data (GPS, camera, lidar, actor tracks) using Scenario Builder for Automated Driving Toolbox. BUILD, EXPORT, or AUGMENT a virtual scenario/scene/map: ego or actor trajectories, trajectory smoothing, OpenCRG road-surface extraction, 3D asset generation, static-object placement, point-cloud georeferencing + elevation, lane-based ego localization, sensor-fusion tracking, scenario-event extraction (cut-ins, hard brakes, near-misses, ADAS disengagements), or export to RoadRunner, drivingScenario, OpenDRIVE, OpenCRG, OpenSCENARIO, or Unreal Engine. Also: log-to-scenario, scenario harvesting, accident/near-miss reconstruction, SOTIF (ISO 21448) and ISO 26262 scenario coverage, USGS-aerial-lidar augmentation, traffic-sign placement, vision-based vehicle classification for actor assets. NOT for raw-data import or multi-sensor sync/crop/offset/timestamp normalization — route those to matlab-import-driving-data.

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Design relational schemas from requirements with normalization, migrations, ERDs, RLS policies, and indexes for PostgreSQL, MySQL, and SQLite. Use when designing new features, reviewing schemas, or adding multi-tenancy.

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Contract intelligence and contract operations workflow skill for Claude and Codex. Guides the full contract lifecycle review process from intake and playbook normalization through clause review, deviation scoring, negotiation planning, approval routing, QA, and action recommendations. Reviews legal, business, operational, compliance, privacy, security, technology, and AI-related risks across contracts and legal documents. Supports NDAs, SaaS agreements, DPAs, procurement contracts, commercial agreements, contract comparisons, redlines, approval packages, clause research, and drafting. Warning-Comprehensive reviews can consume significant Claude/OpenAI tokens, especially for large agreements, playbooks, exhibits, schedules, and multi-document reviews.

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Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained f

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Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.

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standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.

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Multi-route literature expansion + metadata normalization for evidence-first surveys.

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Diagnose and fix concrete MSBuild property defects in projects and existing shared-file hierarchies. USE FOR: conditions, defaults, append versus overwrite, last-write-wins values, OS/TFM checks, portable paths, normalization, and reviews centered on those property defects. Property defects in Directory.Build.* remain in scope, including overwritten values across parent/child imports and conditions that run before TargetFramework is set, even when the fix changes import order or moves a property group to .targets. DO NOT USE FOR: placement-only or import-only requests with no concrete property defect, such as discovering shared files or choosing which file owns a target or customization (use directory-build-organization); item operations; target structure; broad reviews without a concrete property defect; non-MSBuild work.

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Cyber threat intelligence production — the intelligence cycle, IOC extraction/normalization/enrichment, STIX/TAXII and MISP, structured analytic models (Diamond, Kill Chain, ATT&CK), source scoring, actor/campaign tracking, and finished intelligence reporting

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Work on the core package (types, validation, normalization, diff). Use when modifying DSL processing logic, adding new node/edge properties, changing validation rules, or updating the diff algorithm.

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Market data preparation including OHLCV resampling, gap handling, anomaly detection, normalization, and multi-source merging

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scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. Standard scRNA-seq exploration.

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Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.

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Protocols and best practices for western blot quantification and analysis including band detection, normalization, and statistical methods.

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Computational pathology toolkit for whole-slide images (WSIs): load slides, extract tiles, stain normalization, nuclear segmentation, feature extraction, and ML training. Supports H&E and multiplex. For end-to-end pipelines from raw WSIs to quantitative outputs.

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Convert between construction measurement units. Handle metric/imperial conversion, area/volume calculations, and unit normalization for CWICR data.

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Router for FunASR speech workflows: local transcription, subtitles, services, vLLM, normalization, and training/export.

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Base template for Stage2 rebuttal refinement. Use when creating or extending conference-specific Stage2 skills so all venues share the same high-quality writing constraints, JSON output format, and normalization rules.

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