「expression」の検索結果

Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill when: (1) Producing cell embeddings from an AnnData for clustering/integration, (2) Zero-shot or fine-tuned cell-type annotation, (3) Gene-level representation for perturbation/GRN tasks. For probabilistic single-cell models (scVI etc.), use the scvi-tools library.

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Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression. Reach for this skill to integrate scRNA-seq batches, embed cells for clustering, transfer annotations from a reference onto a query, or score differentially expressed genes per cluster. For spatial deconvolution / mapping use the cell2location, DestVI, or Tangram methods instead.

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English LaTeX academic paper assistant for existing `.tex` projects. Use this skill whenever the user wants to compile, lint, audit, or improve an English LaTeX conference or journal paper such as IEEE, ACM, Springer, NeurIPS, or ICML submissions. Trigger even when the user only mentions one paper issue, such as bibliography errors, grammar cleanup, sentence splitting, logic review, expression polishing, translation, title optimization, figure checks, pseudocode review, algorithm block cleanup, de-AI editing, experiment-section review, table structure validation, three-line table generation, abstract structure diagnosis, or journal adaptation. Also trigger for "proofread my paper", "fix my LaTeX", "prepare for submission", "check my manuscript", "improve my writing", "three-line table", "booktabs", "check abstract", "reformat for another journal", "换投", `algorithm2e`, `algorithmicx`, `algpseudocodex`, `Require/Ensure`, or "Algorithm 1" when the user has a .tex file.

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Typst academic paper assistant for existing `.typ` paper projects in English or Chinese. Use this skill whenever the user wants to compile, audit, or improve a Typst paper, including format checks, bibliography validation for BibTeX or Hayagriva, grammar/sentence/logic review, expression polishing, translation, title optimization, pseudocode review, algorithm block cleanup, de-AI editing, experiment-section review, table structure validation, three-line table generation, abstract structure diagnosis, or journal adaptation. Trigger even when the user only mentions one Typst file, one bibliography issue, one pseudocode block, one section rewrite, "three-line table", "check abstract", or "reformat for another journal". Also trigger when the user mentions ".typ files", "typst compile error", "typst export", "typst bibliography", `algorithm-figure`, `lovelace`, or `algorithmic` even without saying the word "Typst" explicitly.

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PROACTIVE SKILL — automatically apply whenever writing, generating, or editing any text that is mainly in Chinese. No user trigger needed. Also use when the user explicitly asks to "fix Chinese", "修改中文", "去翻译腔", "去AI味", "fix Chinese formatting", or "review Chinese text". Eliminates AI-sounding expressions and translation artifacts. Enforces Chinese-English mixed formatting rules (spacing, punctuation, bold formatting).

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Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

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Unified biological database evidence owner. Use for gene annotation, variant clinical significance, cancer mutation evidence, GWAS trait associations, pathway mapping, target-disease evidence, protein structures, protein interaction networks, reference single-cell census queries, and cross-database biological ID mapping. Do not use for full single-cell analysis, bulk RNA-seq differential expression, BAM/VCF processing, protein embedding models, metabolic flux modeling, genomic interval ML, or flow-cytometry file parsing.

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Domain routing and boundary guidance for authorized general injection testing outside SQL injection, including NoSQL, LDAP, XPath, and expression language injection. Use when a task belongs to the general injection domain and needs scope, evidence, pivot, or exit criteria.

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Queries the UniBind database for experimentally validated transcription factor (TF) binding sites. Use when retrieving direct TF-DNA interaction datasets, downloading binding site coordinates (BED/FASTA) for local analysis, or listing available datasets by species, cell line, or TF name. Don't use to query specific intervals, locations, genes, motif models or expression data.

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Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).

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Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression or other analyses. Supports all three ontologies (BP, MF, CC), multiple ID types, and customizable statistical thresholds.

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Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design. Use when prioritizing epitopes for vaccine development or identifying the most immunogenic neoantigens.

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Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.

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Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.

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Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.

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Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when performing DE analysis with edgeR.

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Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular phenotype mediates the genotype-to-phenotype relationship.

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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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SSTI playbook. Use when template expressions, server-side rendering, preview features, or templating engines may evaluate attacker-controlled content.

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Defines and applies visual brand — logo usage, palette, typography, imagery direction, and the guidelines that keep expression consistent across product and marketing surfaces. Use this to establish a brand from scratch, audit whether an existing brand is being applied consistently, build brand guidelines, or decide how a brand should express itself in an unfamiliar format.

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Professional beautification tool for gene expression heatmaps, automatically adds clustering trees, color annotation tracks, and intelligently optimizes label layout.

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Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular...

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Generates complete tumor immune-infiltration-guided bulk-transcriptome diagnostic biomarker and machine-learning research designs from a user-provided cancer type and study direction. Always use this skill whenever a user wants to design, plan, or build a tumor bioinformatics study centered on differential expression, immune infiltration estimation, immune-linked module discovery, consensus feature selection, diagnostic modeling, nomogram construction, clinical association, and optional prognostic extension or validation. Covers five study patterns (immune-cell-first diagnostic workflow, immune-module-to-biomarker workflow, consensus-ML biomarker workflow, diagnostic-plus-prognostic hybrid workflow, translational validation workflow) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path, reference literature pack, and self-critical risk review.

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Generates complete process-related diagnostic biomarker bioinformatics research designs from a user-provided disease context, gene-family or pathway theme, and validation direction. Use when a study centers on process-related genes, DEG and WGCNA integration, machine-learning feature selection, nomogram-based diagnostic modeling, immune infiltration, regulatory-network analysis, and optional external or experimental validation. Covers five study patterns (process-DEG discovery, co-expression-module integration, machine-learning biomarker selection, diagnostic model/nomogram workflow, immune-regulatory interpretation and validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

日本語の概要は準備中です。原文の説明を表示しています。