「expression」の検索結果

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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Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.

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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.

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Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamada-Kawai, hive plots), edge bundling, community-based coloring, and reproducible seeds using NetworkX, PyVis, igraph, and Cytoscape automation. Use when rendering biological networks for static publication, interactive HTML exploration, or Cytoscape-format export.

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Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers. Covers MA plot (with the shrunken-LFC compression effect), volcano (with the apeglm caveat that p-values are unchanged), PCA on VST/rlog (never raw counts), sample distance heatmaps, top-DE-gene heatmaps with the row-scaling trap, dispersion / BCV plot interpretation, p-value histogram diagnostics, plotCounts for individual genes, blind=TRUE vs FALSE rationale, and the n=3 visualization stake. Use when generating DE diagnostic plots, choosing VST vs rlog for visualization, troubleshooting suspicious plot patterns (shifted MA cloud, batch-dominated PCA, anti-conservative p-value histogram), or building a standard QC figure panel.

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Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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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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Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CAI codon-optimized sequences. Use when scoring a gene's codon bias against a host, optimizing a CDS for heterologous expression, or studying synonymous codon selection.

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Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible.

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Performs gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION, PrediXcan, S-PrediXcan, S-MultiXcan, UTMOST, MOSTWAS, kTWAS, EpiXcan, TIGAR-V2, and probabilistic fine-mapping with FOCUS and MA-FOCUS. Use when running TWAS from GWAS sumstats, prioritising candidate causal genes from a GWAS lead locus, picking single-tissue vs cross-tissue models, identifying LD-induced TWAS false positives, choosing ancestry-matched prediction weights, fine-mapping co-regulated TWAS hits, or triangulating TWAS with cis-eQTL Mendelian randomization and colocalization to nominate a causal gene.

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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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Use when building Grafana dashboards backed by Prometheus, Loki, or Tempo, designing PromQL/LogQL queries, wiring template variables, setting alert rules, building SLO dashboards, or maintaining dashboards as code. Triggers: rate() vs increase() confusion, irate vs rate, label_replace, recording rules, alerting rule expressions, multi-dimensional template variables, ad-hoc filters, dashboard JSON model, provisioning via Terraform/grafonnet, p99 / histogram_quantile usage. NOT for Datadog/New Relic dashboards (vendor-specific), Grafana plugin development, or Loki ingestion pipeline tuning.

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This skill suggests medical therapy to block aberrant hormone receptors for bilateral macronodular adrenal hyperplasia (BMAH) when surgery is not preferred or feasible. Consider this approach in patients with confirmed BMAH and evidence of aberrant hormone receptor expression (e.g., GIP, LH/hCG, serotonin) driving cortisol excess.

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Atonement is an expression of care that may arise in an intelligence when its actions contribute to harm.

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Expert-level molecular biology knowledge. Use when working with DNA replication, transcription, translation, gene regulation, cloning, PCR, sequencing, CRISPR, epigenetics, or molecular techniques. Also use when the user mentions 'DNA replication', 'transcription', 'translation', 'gene expression', 'PCR', 'cloning', 'restriction enzyme', 'gel electrophoresis', 'Western blot', 'CRISPR', 'epigenetics', 'promoter', 'enhancer', or 'RNA splicing'.

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Expert-level biochemistry knowledge. Use when working with proteins, enzymes, metabolism, DNA, RNA, carbohydrates, lipids, cell signaling, or bioenergetics. Also use when the user mentions 'enzyme kinetics', 'metabolism', 'glycolysis', 'Krebs cycle', 'DNA replication', 'protein folding', 'amino acids', 'ATP', 'oxidative phosphorylation', 'gene expression', 'lipid bilayer', or 'signal transduction'.

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Type design analysis — encapsulation, invariant expression, usefulness, and enforcement.

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Type design analysis — encapsulation, invariant expression, usefulness, and enforcement.

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Use when configuring Laravel task scheduling — cron expressions, frequency helpers, overlap prevention, maintenance mode, or output handling.

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Use this skill when a user asks to polish, rewrite, humanize, de-AI, localize, or oralize Chinese writing, including short-video scripts, articles, social posts, speeches, newsletters, and personal-IP content. The skill diagnoses “AI味”, preserves the user's meaning, adapts to optional style samples, replaces translation-like phrasing with natural Chinese expression, and outputs a polished version plus concise revision notes.

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Validate and implement Sinclair ZX Spectrum 48K ROM-visible behavior in the EMULATORS repository, including reset and restart vectors, IM1/NMI handling, keyboard scanning and repeat, beeper and tape routines, screen/printer output, channels and streams, BASIC tokenization and execution, expression evaluation, memory movement, system variables, calculator stack, floating-point formats, ROM traps, localized ROM selection, and firmware/hardware timing contracts. Use when Codex reviews or edits ZX Spectrum ROM loading, KERNAL-style traps, keyboard, tape, screen, printer, BASIC files, tokens, system variables, startup, interrupts, or compatibility tests.

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Scans GitHub Actions workflows and CI/CD pipeline configurations for supply chain attack vectors including unpinned actions, script injection via expressions, dependency confusion, and secrets exposure. Uses PyGithub and YAML parsing for automated audit. Use when hardening CI/CD pipelines or investigating compromised build systems.

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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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Apply a set of Rosetta Stone attribute mappings to a Narrative dataset by wrapping them in a one-shot workflow that calls the `CreateRosettaStoneMappingsIfNotExist` task. Consumes the structured output of `/generate-rosetta-stone-mappings`, normalizes the generator's snake_case to the workflow task's camelCase, re-validates every expression against the dataset's current schema, gates on user approval, submits via `narrative_workflows_create`, polls the triggered run, and reports per-mapping created / conflict / failed. Use when: "apply these mappings to dataset N", "create the Rosetta Stone mappings I just generated", "push the mappings I saved earlier to <dataset>", "productionize this mapping list", "submit the suggested_mappings array". (narrative-common)

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