「bulk」の検索結果

Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier handling, VST/rlog transforms, and design formulas including paired, batch, and interaction terms. Use when running bulk DE, choosing DESeq2 over edgeR or limma-voom, building a paired or interaction design, applying LFC shrinkage for ranking or GSEA, choosing Wald vs LRT, troubleshooting padj=NA, picking VST vs rlog, importing salmon/kallisto via tximport, or analyzing prokaryotic RNA-seq.

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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).

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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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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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Build with Aurora DSQL — manage schemas, execute queries, handle migrations, diagnose query plans, diagnose cluster performance, load data, and develop applications with a serverless, distributed SQL database. Covers IAM auth, multi-tenant patterns, MySQL-to-DSQL and PostgreSQL-to-DSQL schema conversion, foreign key constraints, OCC retry patterns, ORM migration (Django/EF Core/Hibernate/Rails/SQLAlchemy), DDL operations, query plan explainability, system diagnostics via CloudWatch AAS, SQL compatibility validation, and bulk data loading. Load before answering DSQL limit or error-code questions; it has limits docs omit. Triggers on phrases like: DSQL, Aurora DSQL, distributed SQL database, serverless PostgreSQL-compatible database, migrate to DSQL, DSQL query plan, DSQL EXPLAIN ANALYZE, DSQL ENUM, DSQL foreign key, DSQL OCC retry, DSQL multi-region, DSQL JSONB, DSQL GIN index, load into DSQL, load CSV into DSQL, bulk load DSQL, aurora-dsql-loader, DSQL slow, DSQL performance, DSQL wait events, DSQL AAS.

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Extract structured data from multiple documents into comparison matrix with citations. Use for bulk document review.

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This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BS

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Execute Python code locally with marketplace API access for 90%+ token savings on bulk operations. Activates when user requests bulk operations (10+ files), complex multi-step workflows, iterative processing, or mentions efficiency/performance.

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Crawl websites and extract content from multiple pages via the Tavily CLI. Use this skill when the user wants to crawl a site, download documentation, extract an entire docs section, bulk-extract pages, save a site as local markdown files, or says "crawl", "get all the pages", "download the docs", "extract everything under /docs", "bulk extract", or needs content from many pages on the same domain. Supports depth/breadth control, path filtering, semantic instructions, and saving each page as a local markdown file.

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Extract structured FF&E specs from a list of product URLs into a schedule. Use to pull or bulk-import product-page data; not for PDF catalogs.

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Provides advanced AWS CLI patterns for managing EC2, Lambda, S3, DynamoDB, RDS, VPC, IAM, and CloudWatch. Generates bulk operation scripts, automates cross-service workflows, validates security configurations, and executes JMESPath queries for complex filtering. Triggers on "aws cli help", "aws command line", "aws scripting", "aws automation", "aws batch operations", "aws bulk operations", "aws cli pagination", "aws multi-region", "aws profiles", "aws cli troubleshooting".

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Bulk grading workflows for Canvas LMS assignments using rubrics. Covers single grading, batch grading, and code execution strategies with safety-first dry runs.

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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).

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Python-first workflow for bulk RNA-seq expression intake, normalization, sample QC, and downstream-ready matrices.

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Bulk-regenerate broken test selectors after a UI refactor or redesign. Detects drift between old and new DOM with an aria-snapshot diff, maps old locators to new equivalents using role-first + region scoping, validates against the new build, and produces a single PR with grouped per-file selector updates and per-change evidence. Assumes Playwright >= 1.50 (trace viewer DOM-snapshot panel, getByRole filtering, ariaSnapshot). Use when: "UI refactor broke tests," "redesign broke tests," "bulk update selectors," "regenerate selectors after refactor," "selector drift," "fix N broken tests after redesign." Not for: healing one flaky test at runtime — use test-reliability. Not for: writing a new test suite from scratch — use playwright-automation. Not for: re-recording tests after a framework switch (Selenium to Playwright) — use test-migration. Related: test-reliability, playwright-automation, test-migration, ci-cd-integration, visual-testing.

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Import structured data into Neo4j — LOAD CSV, CALL IN TRANSACTIONS, neo4j-admin database import full (offline bulk), apoc.load.csv/json, apoc.periodic.iterate, driver batch writes. Covers method selection, header file format, type coercion, null handling, ON ERROR modes, CONCURRENT TRANSACTIONS, pre-import constraint setup, and post-import validation. Use when importing CSV/JSON/Parquet files, migrating relational data to graph, or bulk-loading large datasets. Does NOT handle unstructured document/PDF/vector chunking pipelines — use neo4j-document-import-skill. Does NOT handle live app write patterns (MERGE/CREATE) — use neo4j-cypher-skill. Does NOT handle neo4j-admin backup/restore/config — use neo4j-cli-tools-skill.

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Batch download academic paper full-text (PDF/XML) from a list of DOIs. Handles 25 DOI prefixes across 19 publisher families via three layered routes: (1) publisher TDM APIs requiring institutional subscription (Elsevier ScienceDirect, Wiley Online, Springer Nature), (2) Open Access sources (Crossref, Unpaywall, OpenAlex), and (3) a browser-based fallback for paywalled publishers without TDM access (ACS, RSC, IEEE, AIP, IOP, APS, Annual Reviews, T&F, Chinese journals). Browser fallback offers two routes — Route A drives the user's logged-in Chrome via the OpenClaw `browser` tool with `profile="user"` (best for interactive sessions), Route B uses the standalone `auto-paper-harvester` CLI with its built-in Playwright (best for unattended bulk runs). Use when the user wants to harvest, scrape, fetch, or bulk-download papers from a DOI list, savedrecs export, or Excel; or wants to fill missing full-text PDFs for an existing literature collection. Triggers on phrases like "批量下载文献", "下载全文", "harvest papers", "scrape full text", "TDM API", "下载 Elsevier 全文", "Wiley 批量下载", "下载 PDF".

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Bulk-refresh research entries in ./research/ using parallel research-curator agents. Use when /refresh-research is invoked, stale research needs updating, or bulk re-verification of research entries is requested. Inventories entries by review date and age, runs RT-ICA pre-flight, spawns agents in waves of 5, then validates, reviews, and commits through research-curator. Supports --all, --stale, --category, --layer, and --dry-run flags.

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Parallel map-reduce bulk ingest for large source sets. Map phase dispatches read-only knowledge-extractor agents (≤N-wide, default Haiku) emitting per-source JSON extracts; Python routes extracts by target library file (fuzzy-merging new topics, pre-allocating new files, flagging oversized topics); reduce phase dispatches one agent-knowledge-updater per file (parallel, one writer per file); single shelf-index rebuild + one log.md entry. Resumable. Supersedes kb-ingest-batch.

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Build with Aurora DSQL — manage schemas, execute queries, handle migrations, diagnose query plans, load data, and develop applications with a serverless, distributed SQL database. Covers IAM auth, multi-tenant patterns, MySQL-to-DSQL and PostgreSQL-to-DSQL schema conversion, FK replacement code generation, OCC retry patterns, ORM migration (Django/Hibernate/Rails), DDL operations, query plan explainability, SQL compatibility validation, and bulk data loading. Triggers on phrases like: DSQL, Aurora DSQL, distributed SQL database, serverless PostgreSQL-compatible database, migrate to DSQL, DSQL query plan, DSQL EXPLAIN ANALYZE, DSQL ENUM, DSQL foreign key, DSQL OCC retry, DSQL multi-region, DSQL JSONB, DSQL GIN index, load into DSQL, load CSV into DSQL, bulk load DSQL, aurora-dsql-loader.

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Use when sending transactional emails (welcome messages, order confirmations, password resets, receipts), notifications, or bulk emails via Resend API. Triggers on "send email", "transactional email", "welcome email", "Resend API", "password reset email", "order confirmation", "receipt email", "notification email", "bulk email send".

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Focused single-target audit of one Gaia skill, named skill, or real-skill catalog item. Use this skill when: auditing a specific skill by ID or name, a skill looks overpromoted, evidence feels thin or dead, a contributor's skill seems outdated or superseded, the rank doesn't match the source quality, evidence is mapped to the wrong Evidence Type, a skill at 3★+ is missing a working GitHub link, someone asks "does this skill deserve its stars?", or you want the smallest possible correction with validation — not a bulk sweep. This is NOT for bulk curation passes (use /gaia-curate for that) or meta-level registry sweeps (use /gaia-meta-audit). It is specifically for "fix this one skill, get it right."

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