「bulk」の検索結果

Use when building a weighted gene co-expression network from a bulk expression matrix and a sample group file, filtering variable genes by MAD, identifying co-expression modules with WGCNA, correlating modules with traits, and exporting module-level plots and gene tables. NOT for single-cell RNA-seq, differential expression testing, methylation analysis, or datasets that are too small for WGCNA after quality control.

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Run immune pathway GSVA or ssGSEA analysis from a bulk expression matrix, a sample group file, and a local immune Reactome gene-set table, then export differential pathway results and a heatmap for two-group comparison.

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Use when validating an existing prognostic risk signature on an external bulk expression cohort with survival outcomes, producing risk scores, Kaplan-Meier curves, risk distribution plots, heatmap, and time-dependent ROC curves. NOT for: model training, feature selection, nomogram construction, calibration analysis, or single-cell data.

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Use this skill to run GSVA or ssGSEA pathway-level differential analysis from a bulk expression matrix and a sample group file, then generate a heatmap from the saved GSVA result object. Trigger keywords: GSVA, ssGSEA, pathway enrichment, KEGG pathway analysis, MSigDB. NOT for: gene-level differential expression, single-cell analysis, methylation analysis, clinical diagnosis.

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Use when estimating relative immune cell infiltration from a bulk expression matrix with a CIBERSORT-style nu-SVR deconvolution workflow based on an LM22 signature matrix, comparing one case group against one control group, and generating structured tables plus immune-fraction plots. NOT for single-cell RNA-seq, spatial data, clinical diagnosis, or workflows that require the original hosted CIBERSORT web service.

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Use when filtering genes with high missingness and then imputing missing values in a bulk expression matrix with group-aware KNN through DMwR2, where donor samples are restricted by one annotation column before imputation. For strata with 10 or fewer samples, the script falls back to row-wise direct filling with mean or median. NOT for: single-cell data, multi-column stratification, non-tabular inputs, network access, or interactive workflows.

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Use when performing GO and KEGG enrichment on a gene list from bulk RNA-seq or microarray studies, then generating a combined GO/KEGG dot chart. NOT for single-cell RNA-seq, methylation data, or non-expression data.

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Use when building a sample-level hierarchical clustering dendrogram from a bulk expression matrix and sample annotation table, especially for QC, batch inspection, or sample similarity assessment. Trigger keywords: hierarchical clustering, dendrogram, sample QC, batch inspection, sample similarity. NOT for: differential expression testing, gene clustering heatmaps, single-cell clustering workflows.

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。

Use when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory analysis. NOT for count-model normalization such as TPM/DESeq2 size factors, batch correction, or single-cell preprocessing.

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Use when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization. NOT for: differential expression analysis, single-cell clustering workflows, or non-expression tables.

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Use when correcting batch effects in merged bulk expression matrices with sample-level batch metadata while preserving biological group structure and generating before-and-after QC plots. NOT for: single-cell integration, raw FASTQ processing, differential expression without batch labels, or datasets without biological groups.

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Use this skill to compute ESTIMATE immune-related microenvironment scores from a bulk expression matrix, generate an ESTIMATE score heatmap, and optionally generate group-wise ESTIMATE score boxplots plus significance tables when a sample group file is supplied. Trigger keywords: ESTIMATE, immune score, stromal score, tumor microenvironment score. NOT for: immune cell deconvolution, single-cell analysis, differential expression, clinical diagnosis.

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Use when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap. Triggers include DEG analysis, volcano plot, clustered heatmap, limma-based two-group comparison, and case-vs-control screening. NOT for single-cell RNA-seq, multi-group contrasts, count-model workflows such as DESeq2/edgeR, or non-expression omics data.

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Use when selecting predictive genes or other molecular features from bulk expression matrices for binary case-vs-control classification with elastic net logistic regression, including coefficient path and cross-validation plots. Trigger keywords: elastic net, glmnet, feature selection, binary classification, lambda.min, lambda.1se. NOT for: survival/Cox modeling, multiclass outcomes, single-cell data, or non-expression tables.

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Use when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and heatmap visualization. NOT for:single-cell RNA-seq, methylation analysis, non-expression data.

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Apply to any non-trivial work, not just bulk work: edits, migrations, analyses, checks. Build the tool that does it or proves it (codemod, script, generator, or a skill your subagents follow) instead of working by hand. The tool is the artifact a reviewer can rerun.

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Apply when context is filling up: large outputs, long files, repeated reads, fan-out planning. Route bulk to subagents; keep summaries in the main thread, not raw payloads.

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Use this skill for setting up vector similarity search with pgvector for AI/ML embeddings, RAG applications, or semantic search. **Trigger when user asks to:** - Store or search vector embeddings in PostgreSQL - Set up semantic search, similarity search, or nearest neighbor search - Create HNSW or IVFFlat indexes for vectors - Implement RAG (Retrieval Augmented Generation) with PostgreSQL - Optimize pgvector performance, recall, or memory usage - Use binary quantization for large vector datasets **Keywords:** pgvector, embeddings, semantic search, vector similarity, HNSW, IVFFlat, halfvec, cosine distance, nearest neighbor, RAG, LLM, AI search Covers: halfvec storage, HNSW index configuration (m, ef_construction, ef_search), quantization strategies, filtered search, bulk loading, and performance tuning.

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Apply when context is filling up: large outputs, long files, repeated reads, fan-out planning. Route bulk to subagents; keep summaries in the main thread, not raw payloads.

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。

Apply to any non-trivial work, not just bulk work: edits, migrations, analyses, checks. Build the tool that does it or proves it (codemod, script, generator, or a skill your subagents follow) instead of working by hand. The tool is the artifact a reviewer can rerun.

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。

Search LCSC Electronics for electronic components — find parts by LCSC number (Cxxxxx) or MPN, check stock/pricing, download datasheets, analyze specifications. Sister company to JLCPCB, same parts library. Sync and maintain a local datasheets directory for a KiCad project, or use batch MPN-list seeding (`--mpn-list`) for bulk workflows without a project. No API key needed — uses the free jlcsearch community API. Use this skill when the user mentions LCSC, JLCPCB parts library, JLCPCB assembly parts, production sourcing, Cxxxxx part numbers, needs to find LCSC equivalents for parts, is preparing a BOM for JLCPCB assembly, or wants to download datasheets and LCSC is available. For package cross-reference tables and BOM workflow, see the `bom` skill.

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Search Mouser Electronics for electronic components — secondary source for prototype orders. Find parts, check pricing/stock, download datasheets, analyze specifications. Use with KiCad for BOM creation and part selection. Also supports batch MPN-list seeding (`--mpn-list`) for bulk datasheet workflows without a KiCad project. Use this skill when the user specifically mentions Mouser, when DigiKey is out of stock or has worse pricing, when comparing prices across distributors, or when searching for parts that DigiKey doesn't carry. For package cross-reference tables and BOM workflow, see the `bom` skill.

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Search Newark, Farnell, and element14 for electronic components — find parts by MPN or distributor part number, check pricing/stock, download datasheets, analyze specifications. One unified API covers all three storefronts (Newark for US, Farnell for UK/EU, element14 for APAC). Free API key, simple query-parameter auth, no OAuth. Datasheets download directly from farnell.com CDN with no bot protection. Sync and maintain a local datasheets directory for a KiCad project, or use batch MPN-list seeding (`--mpn-list`) for bulk workflows without a project. Use this skill when the user mentions Newark, Farnell, element14, needs parts from a non-US distributor, wants to compare pricing across regions, or needs datasheets from a source that doesn't require complex API auth. For package cross-reference tables and BOM workflow, see the `bom` skill.

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Search DigiKey for electronic components and download datasheets — primary source for prototype orders and the preferred API method for fetching datasheets. Find parts by keyword or MPN, check pricing/stock, download datasheets via API, analyze specifications. Sync and maintain a local datasheets directory — extract components from schematics, download missing datasheets, keep them up to date. Also supports batch MPN-list seeding (`--mpn-list`) for bulk workflows without a KiCad project. Use when the user asks about electronic components, part specs, datasheets, pricing, stock, footprints, or needs to download a datasheet — even without mentioning "DigiKey". Also for "sync datasheets", "download datasheets for my board/project", or mentions a datasheets directory. DigiKey is the default distributor for prototyping. For BOM workflows, see the bom skill.

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。