'batch' 검색 결과

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

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Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy URL migration (2022), the new JSON schema layout, and bulk-pull patterns.

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Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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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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Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and when to defect to de novo computation.

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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

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Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.

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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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Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract, SES), k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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Apply recognition-primed decision making to agents operating under time pressure, uncertainty, and ambiguous cues. Use for situation assessment, RPD-style action selection, and decision-support design in operational settings. NOT for batch optimization, static planning with full information, or tasks where exhaustive search is cheap and harmless.

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Apply recognition-primed decision making to agents operating under time pressure, uncertainty, and ambiguous cues. Use for situation assessment, RPD-style action selection, and decision-support design in operational settings. NOT for batch optimization, static planning with full information, or tasks where exhaustive search is cheap and harmless.

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Expert data engineer for ETL/ELT pipelines, streaming, data warehousing. Activate on: data pipeline, ETL, ELT, data warehouse, Spark, Kafka, Airflow, dbt, data modeling, star schema, streaming data, batch processing, data quality. NOT for: API design (use api-architect), ML training (use ML skills), dashboards (use design skills).

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Expert in background job processing with Bull/BullMQ (Redis), Celery, and cloud queues. Implements retries, scheduling, priority queues, and worker management. Use for async task processing, email campaigns, report generation, batch operations. Activate on "background job", "async task", "queue", "worker", "BullMQ", "Celery". NOT for real-time WebSocket communication, synchronous API calls, or simple setTimeout operations.

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Data structures and serialization formats for agent-to-agent communication. Covers message envelopes, structured output schemas, capability declarations, task handoff payloads, error/retry signaling, and context windows as data structures. Compares the version-pinned A2A, MCP, and JSON-RPC role boundaries covered by this bundle; OpenAI and LangChain-specific APIs require their own current sources. Teaches when to use rigid schemas versus free-form content with validation, typed versus untyped boundaries, and streaming versus batch. Activate on: "agent message format", "agent communication schema", "agent-to-agent protocol", "A2A protocol", "MCP message format", "structured output for agents", "agent interop", "interchange format", "agent serialization", "task handoff format", "capability declaration". NOT for: what agents say to each other (use agent-conversation-protocols), orchestration topology (use multi-agent-coordination), building agent infrastructure (use agentic-infrastructure-2026).

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Doctrine for fixing TypeScript errors against generated types (database.types.ts, api-types.ts). Use when fixing tsc or type-check failures or a type-errors batch, writing supabase .rpc()/.from() calls or DB shape guards, errors mention Json/unknown/Database, or you are tempted to cast or suppress.

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Coordinator for the fleet that repairs and independently certifies registered UI surfaces through Work Loop claims. Use for pilot batches, recurring certification, repair rounds, or retroactive rechecks after surface-check rules change. NOT for one assigned surface (use surface-check).

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Discovery batch that grows the Provider Access Launch queue. Use when asked to find more user-connected OAuth, API, API-key, remote MCP, marketplace, or partner-access campaigns for a capability, provider family, MCP/plugin catalog, or competitive gap. NOT for client Local Listings distribution.

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No-loss protocol for changing an existing mandate's output contract. Use when changing what an agent or mandate emits or how it is typed: binding a kind, declaring output_kind, kind-backfill batches, provision reconciliation, or any make-this-contract-honest sweep. NOT for creating a new agent (use create-agent).

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Use when the user asks to generate or edit images via the OpenAI Image API (for example: generate image, edit/inpaint/mask, background removal or replacement, transparent background, product shots, concept art, covers, or batch variants); run the bundled CLI (`scripts/image_gen.py`) and require `OPENAI_API_KEY` for live calls.

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This skill should be used when the user asks to "これらのIssueを全部実装して", "implement these issues autonomously", "Issue一覧を自動で片付けて", "これらのタスクを順番に実装してPRにして", or provides a list of GitHub Issue numbers/URLs for autonomous batch implementation. Fetches all specified Issues, resolves dependency order, then iterates through each — creating a worktree, implementing, and opening a PR — without user intervention.

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Hands work to a local model served by LM Studio and verifies what comes back. Trigger to offload, delegate or batch work to a local, offline or on-device model; to queue unattended runs that keep only what passes; to ask which installed model fits a job or whether to switch; to size a task before delegating; when a local model returns nothing, repeats itself or drifts on a long list; when LM Studio shares the GPU with an image tool, or to free its hold; or say lmstudiorunner (audit, size, queue, run, status). Reads models from the live LM Studio API. Cloud model picks and prompt text are promptwright's; a schedule's guardrails agentwright's.

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Transcribes local audio and video to txt, srt, vtt and json with timestamps using whisper.cpp, and proves which backend ran. Trigger to transcribe, caption or subtitle a recording, meeting, podcast or video locally; to pick a Whisper model for this GPU or estimate a batch; when a transcript is empty, cut short or repeating; when Whisper ran on the CPU or a pasted log must prove the GPU ran; when it shares the GPU with LM Studio or ComfyUI; or say whisperrunner (audit, check, plan, run, status, refresh). Never a cloud API or a download. Voice-overs are comfyrunner's; clips and burned-in captions obsrunner's; game audio soundsmith's; summarising transcripts lmstudiorunner's.

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