「expression」の検索結果

Design and review Action Scheduler jobs in WordPress plugins using Action Scheduler 3.9.x public APIs - async, single, recurring, and cron-expression actions; action_scheduler_init load timing; hook/args/group naming; unique and priority parameters; idempotent callbacks; chunked workloads; activation/deactivation cleanup; WooCommerce-bundled or standalone dependency usage; admin and WP-CLI debugging; queue runner limits; and safe operational troubleshooting. Use when a plugin schedules background jobs with as_enqueue_async_action, as_schedule_single_action, as_schedule_recurring_action, as_schedule_cron_action, as_get_scheduled_actions, or integrates with WooCommerce background queues.

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Comprehensive regular expressions guide covering character classes, quantifiers, anchors, groups, lookahead/lookbehind, common patterns (email, URL, IP, phone, dates, semver), ReDoS prevention, Unicode support, flags, debugging, and when NOT to use regex.

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GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). Load matrix, filter by TFs, infer TF-target-importance links, save network. Dask-parallelized to single-cell scale. Core SCENIC component.

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Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

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AI-powered design of armored CAR-T cells with cytokine/chemokine expression for enhanced solid tumor efficacy, including IL-12, IL-15, IL-18, and IL-7 armoring strategies.

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Expert en n8n avancé (workflows, nodes, expressions, webhooks, self-hosted, custom nodes, scaling, error handling)

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Performs numerical and symbolic mathematics using NumPy, SciPy, SymPy, and mpmath. Use when the user needs linear algebra, arrays, optimization, integration, ODEs, symbolic expressions, equation solving, or arbitrary-precision arithmetic.

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Apply modern Swift language patterns and idioms for non-concurrency, non-SwiftUI code. Covers if/switch expressions (Swift 5.9+), typed throws (Swift 6+), result builders, property wrappers, opaque and existential types (some vs any), guard patterns, Never type, Regex builders (Swift 5.7+), Codable best practices (CodingKeys, custom decoding, nested containers), modern collection APIs (count(where:), contains(where:), replacing()), FormatStyle (.formatted() on dates, numbers, measurements), and string interpolation patterns. Use when writing core Swift code involving generics, protocols, enums, closures, or modern language features.

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Parse Windows PowerShell Script Block Logs (Event ID 4104) from EVTX files to detect obfuscated commands, encoded payloads, and living-off-the-land techniques. Uses python-evtx to extract and reconstruct multi-block scripts, applies entropy analysis and pattern matching for Base64-encoded commands, Invoke-Expression abuse, download cradles, and AMSI bypass attempts.

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GitHub Actions security review for workflow exploitation vulnerabilities. Use when asked to "review GitHub Actions", "audit workflows", "check CI security", "GHA security", "workflow security review", or review .github/workflows/ for pwn requests, expression injection, credential theft, and supply chain attacks. Exploitation-focused with concrete PoC scenarios.

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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.

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Calculates statistical power for high-dimensional genomics experiments (bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, methylation, proteomics) under negative-binomial count models using RNASeqPower, PROPER, and simulation via powsimR, distinguishing per-gene from marginal (transcriptome-wide) power, the role of mean expression and dispersion, and the sequencing-depth-versus-replicate tradeoff. Covers simulation as the honest default for overdispersed counts, FDR-aware average power versus single-test power, observed/post-hoc power as an anti-pattern, and the winner's-curse / Type-S / Type-M consequences of underpowering. Use when planning replicate number for a sequencing experiment, deciding whether to add depth or samples, choosing closed-form versus simulation power, estimating power from pilot dispersions, or justifying replication in a grant. For clinical-trial power see clinical-biostatistics/power-and-sample-size; for the inverse sample-size question see experimental-design/sample-size.

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End-to-end small RNA-seq analysis from FASTQ to differential miRNA expression and target prediction. Use when analyzing miRNA, isomiR, tRF, or piRNA sequencing data through preprocessing, quantification, discovery, DE, and targets.

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Orchestrates an end-to-end immune-repertoire pipeline from FASTQ to clonotypes, diversity, overlap, somatic hypermutation and lineages, routing on two forks. Use when deciding bulk vs single-cell (bulk amplicon/RNA-seq -> MiXCR analyze preset -> VDJtools/immunarch depth-normalized diversity and overlap -> figures; 10x paired VDJ -> MiXCR 10x preset or Cell Ranger -> scirpy gene-expression integration, chain QC, clonotype clusters); and TCR vs BCR (TCR -> exact CDR3-nt+V/J clonotypes, VDJtools diversity is fine; BCR -> somatic hypermutation makes exact clonotypes wrong -> Immcantation distToNearest/findThreshold clonal clustering, germline reconstruction, SHM, Dowser lineages); selecting the MiXCR 4.x preset by chemistry and activating its license; downsampling to equal depth before comparing diversity or overlap; and optionally annotating antigen specificity.

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End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visualization. Use when running RNA-seq from FASTQ to DE results.

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Builds diagnostic and prognostic classifiers on omics feature matrices with regularized logistic regression, random forest, and gradient-boosted trees, handling the p>>n regime, batch shortcut learning, class imbalance, and probability calibration. Use when building a classifier from expression, methylation, or variant data, choosing an algorithm for high-dimensional small-n data, or diagnosing a suspiciously perfect AUC. For unbiased evaluation see machine-learning/model-validation; for feature selection see machine-learning/biomarker-discovery; for time-to-event outcomes see machine-learning/survival-analysis.

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End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, leakage-safe cross-validation, calibration, and SHAP interpretation. Use when building and validating diagnostic or prognostic biomarker signatures from omics data.

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Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on Toil/Arvados/Calrissian. Use when deciding CWL (portability/provenance/regulated) vs Nextflow/WDL/Snakemake; declaring secondaryFiles for indexed companions (.bai/.fai/.dict/.tbi and the caret rule); putting resources/containers under requirements (must-hold) vs hints (advisory) to avoid silent OOM; choosing scatterMethod (dotproduct vs flat_/nested_crossproduct); preferring $(...) parameter refs over ${...} JavaScript for portability; pinning DockerRequirement images; or emitting a CWLProv provenance object for audited/clinical settings.

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Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

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Triage a GitHub issue that already has the cc-issue-created label and is assumed ready to start. Inspect the comment history first to decide whether human confirmation is needed (cc-need-human-check, highest priority — reserved for issue-level deadlock, or for confirmation items answer-issue-questions already investigated and explicitly marked unanswerable); otherwise close the issue as not needed, delegate unanswered confirmation items in the last comment or the description to answer-issue-questions (cc-answer-issue-questions), refresh a description stale relative to settled comment-history content (cc-update-issue), or move to execution (cc-exec-issue). Any UI-changing issue is routed to the design-first flow (cc-create-ui-design) before execution; the exceptions are an issue whose description already names the .pen design to implement against, and a minor UI change that introduces no new visual decision (no new screen/section, no layout change, no new reusable component, no visual expression outside existing design tokens/components). Design files are never edited in the implementation PR. Dependency checks are out of scope.

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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.

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Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for personalized cancer vaccines and checkpoint biomarkers. Encodes the field's hard truth that binding prediction is the easy, near-solved part and single-digit-percent PPV lives downstream — so it centers clonality/CCF, HLA LOH (the silent invalidator), expression, proximal-variant phasing, agretopicity/foreignness quality, and the predicted->presented->immunogenic validation tiers. Use when nominating vaccine targets, ranking neoantigens, or building a tumor-to-candidate pipeline. Binding details in mhc-binding-prediction; ranking in immunogenicity-scoring.

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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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