「single」の検索結果

Start (or restart) a local multi-node Temps cluster using Docker-in-Docker — one control plane + 3 worker nodes, each a privileged DinD container running its own dockerd + `temps agent`, wired with the real multi-host overlay (VXLAN, compute_cidr allocation) via `tools/dev-cluster/` in whichever checkout/worktree you run it from. Invoke when the user says "start the temps cluster", "spin up a multi-node dev cluster", "test this with multiple workers", "bring up worker nodes locally", "docker in dind cluster", or wants to verify cross-node behavior (node targeting, cluster DNS, overlay networking, node join/mTLS) that a single-node `start-temps` server cannot exercise. Distinct from `start-temps` (single-node, native binary, port-slot based) and `start-temps-ee` (single-node EE binary) — this is the only path that actually has more than one node.

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Deep single-page SEO analysis covering on-page elements, content quality, technical meta tags, schema, images, and performance. Use when user says "analyze this page", "check page SEO", "single URL", "check this page", "page analysis", or provides a single URL for review.

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Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.

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Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.

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。

Single page smart extraction - articles, docs, blog posts to clean markdown

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Detects MSBuild projects with conflicting OutputPath or IntermediateOutputPath. USE FOR: builds failing with 'Cannot create a file when that file already exists', 'The process cannot access the file because it is being used by another process', intermittent build failures that succeed on retry, or missing/overwritten outputs in multi-project or multi-targeting builds where bin/obj (or project.assets.json) collide. Common causes: shared OutputPath, missing AppendTargetFrameworkToOutputPath, extra global properties (e.g. PublishReadyToRun), or SetTargetFramework on a ProjectReference to a single-targeting project. DO NOT USE FOR: file access errors unrelated to MSBuild (OS-level locking), single-project single-TFM builds, non-MSBuild build systems.

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Multi-modal single-cell analysis with muon/MuData. Joint RNA+ATAC (10x Multiome), CITE-seq (RNA+protein), other multi-omics. MuData holds per-modality AnnData with shared obs. WNN joint embedding, per-modality preprocessing, MOFA factor analysis. Use scanpy-scrna-seq for single-modality RNA; use muon when combining 2+ omics from the same cells.

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Apply single-cell rna qc in reproducible local data workflows with version-aware APIs, explicit assumptions, and validation. Use when the user chooses single-cell rna qc or its strengths fit the task.

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End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate Pearson, CEGv2 PR-AUC, copy-number artifact), method-appropriate hit calling across MAGeCK RRA/MLE, BAGEL2, drugZ, JACKS, and Chronos, cancer-cell-line copy-number correction (CRISPRcleanR / Chronos), batch correction for multi-batch screens, and the specialized branches for combinatorial paralog screens, single-cell Perturb-seq, base-editor variant-function screens, prime-editor screens, and in vivo bottleneck-aware screens. Use when analyzing any pooled CRISPR screen end-to-end, choosing the correct hit-calling method by experimental design, integrating copy-number correction into the pipeline, or branching the workflow for single-cell, combinatorial, base-editor, prime-editor, or in vivo variants.

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Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating Seurat objects and AnnData objects, and converting between formats. Use when loading, saving, or converting single-cell data formats.

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Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PCA, computing neighbors, clustering with Leiden/Louvain algorithms, generating UMAP/tSNE embeddings, and visualizing clusters. Use when performing dimensionality reduction and clustering on single-cell data.

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。

Deep single-page SEO analysis covering on-page elements, content quality, technical meta tags, schema, images, and performance. Use when user says "analyze this page", "check page SEO", "single URL", "check this page", "page analysis", or provides a single URL for review.

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Design a single-point rubric with one criterion and open columns for evidence. Use for student self-assessment, peer feedback, teacher formative feedback, or pre-task planning. Works with any learning target, with or without a band system.

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Parallel SDLC batch runner. Analyzes a list of independent task descriptions, groups them by heuristic file-conflict prediction, dispatches one worktree-isolated background agent per task (each running the full pipeline-orchestrator: BA → Dev → QA → Sec → Docs), and aggregates results into a single batch summary. Use when: - `/sdlc:batch` invokes this skill after parsing its arguments (Step 2 of commands/batch.md) - You have 2+ independent feature/fix descriptions to run through the SDLC pipeline in parallel Do NOT use for: - A single task (use pipeline-orchestrator directly via /sdlc:start) - Tasks that must share a single working tree (this skill isolates each task in its own git worktree)

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"Apply case study research design (Yin) to investigate how and why questions within real-life contexts using single or multiple case designs and triangulation. Use this skill when the user needs to choose between single and multiple case designs, apply holistic versus embedded units of analysis, triangulate evidence from multiple sources, or when they ask 'how should I structure a case study', 'single or multiple cases', or 'how do I ensure validity in case research'.".

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Orchestrates single-task implementation pipeline: plan → test → build → review. Shipping is an explicit follow-up. Use for feature work, plan execution, or fixes scoped to a single task. NOT for green-field product builds (see mk:autobuild); NOT for auto-invoked workflow orchestration (see mk:workflow-orchestrator).

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。

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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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.

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 working with Singlestore — singleStore (MemSQL) workspace management, pipeline status, query tuning, memory analysis, and cluster health.

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。

シングルエージェントで計画書/タスクを順次実装する開発フロー。「シングルフロー」「shiiman-workflow:single」「1 人で実装」「順次実装」「シングルで実装して」「一人で開発」などで起動。Issue/PR まで作るかは発話・引数から判断し、曖昧なら確認する。

End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate Pearson, CEGv2 PR-AUC, copy-number artifact), method-appropriate hit calling across MAGeCK RRA/MLE, BAGEL2, drugZ, JACKS, and Chronos, cancer-cell-line copy-number correction (CRISPRcleanR / Chronos), batch correction for multi-batch screens, and the specialized branches for combinatorial paralog screens, single-cell Perturb-seq, base-editor variant-function screens, prime-editor screens, and in vivo bottleneck-aware screens. Use when analyzing any pooled CRISPR screen end-to-end, matching the hit-calling method to the experimental design, integrating copy-number correction into the pipeline, or branching the workflow for single-cell, combinatorial, base-editor, prime-editor, or in vivo variants.

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。

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.

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。

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.

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。

Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are the chemistries that give per-cell isoform structure. Tools include MARVEL (R, Smart-seq integrated), BRIE2 (Bayesian PSI with regulatory features and ELBO_gain test), scQuint (junction-cluster, plate-based; not for 10X), SpliZ (annotation-free Z-score), Psix (graph-smoothness regulated AS), and Sierra (alternative polyadenylation, often confused with AS). Use when analyzing isoform usage in scRNA-seq, identifying cell-type-specific splicing, or determining whether scRNA-seq chemistry supports splicing analysis at all.

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。