「calling」の検索結果

Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.

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Add, review, or fix JavaScript interop in Blazor components. USE FOR: calling JavaScript from Blazor, calling .NET from JavaScript, collocated .razor.js modules, IJSRuntime, IJSObjectReference lifecycle, DotNetObjectReference, ElementReference, timing rules for when JS is available, IAsyncDisposable disposal of JS references, server-side JS interop safety. DO NOT USE FOR: general Blazor component authoring without JS interop needs (use author-component), forms (use collect-user-input).

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Build AI-enabled .NET applications with Semantic Kernel using services, plugins, prompts, and function-calling patterns that remain testable and maintainable. USE FOR: adding AI-driven prompts, plugins, or orchestration to a .NET app; reviewing kernel construction, service registration, or plugin usage; building function-calling. DO NOT USE FOR: unrelated stacks; generic tasks that do not need this specific guidance. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats. Core post-variant-calling: quality filtering, multi-sample merging, rsID annotation, genotype extraction. Samtools companion in HTSlib. Use GATK for complex indel realignment during calling; use VCFtools for population genetics stats.

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Provides LangChain4j patterns for implementing MCP (Model Context Protocol) servers, creating Java AI tools, exposing tool calling capabilities, and integrating MCP clients with AI services. Use when building a Java MCP server, implementing tool calling in Java, connecting LangChain4j to external MCP servers, or securing tool exposure for agent workflows.

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Provides and generates LangChain4j tool and function calling patterns: annotates methods as tools with @Tool, configures tool executors, registers tools with AiServices, validates tool parameters, and handles tool execution errors. Use when building AI agents that call tools, define function specifications, manage tool responses, or integrate external APIs with LLM-driven applications.

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This skill should be used when the user asks about "bun:ffi", "foreign function interface", "calling C from Bun", "native libraries", "dlopen", "shared libraries", "calling native code", or integrating C/C++ libraries with Bun.

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End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller. Use when calling variants from raw sequencing reads.

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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.

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 CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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 learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinical or research applications.

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。

Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.

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。

Answer questions about the AI SDK and help build AI-powered features. Use when developers: (1) Ask about AI SDK functions like generateText, streamText, ToolLoopAgent, embed, or tools, (2) Want to build AI agents, chatbots, RAG systems, or text generation features, (3) Have questions about AI providers (OpenAI, Anthropic, Google, etc.), streaming, tool calling, structured output, or embeddings, (4) Use React hooks like useChat or useCompletion. Triggers on: "AI SDK", "Vercel AI SDK", "generateText", "streamText", "add AI to my app", "build an agent", "tool calling", "structured output", "useChat".

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Tools are how AI agents interact with the world. A well-designed tool is the difference between an agent that works and one that hallucinates, fails silently, or costs 10x more tokens than necessary. This skill covers tool design from schema to error handling. JSON Schema best practices, description writing that actually helps the LLM, validation, and the emerging MCP standard that's becoming the lingua franca for AI tools. Key insight: Tool descriptions are more important than tool implementations. The LLM never sees your code - it only sees the schema and description. Use when "agent tool, function calling, tool schema, tool design, mcp server, mcp tool, tool use, build tool for agent, define function, input_schema, tool_use, tool_result, agents, tools, function-calling, mcp, json-schema, anthropic, openai, llm-tools" mentioned.

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Comprehensive patterns for building AI-powered code generation tools, code assistants, automated refactoring, code review, and structured output generation using LLMs with function calling and tool use. Use when "code generation, AI code assistant, function calling, structured output, code review AI, automated refactoring, tool use, code completion, agent code, " mentioned.

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Expert in designing and building autonomous AI agents. Masters tool use, memory systems, planning strategies, and multi-agent orchestration. Use when "build agent, AI agent, autonomous agent, tool use, function calling, multi-agent, agent memory, agent planning, langchain agent, crewai, autogen, claude agent sdk, ai-agents, langchain, autogen, crewai, tool-use, function-calling, autonomous, llm, orchestration" mentioned.

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LLM 集成全流程。覆盖 OpenAI / Anthropic / Google / 开源模型接入、Prompt 工程、 Function Calling、Agent 编排、Token 优化、安全防护、生产化部署。 触发关键词：LLM、GPT、Claude、Gemini、Prompt、Function Calling、Tool Use、 Agent、Chain、Structured Output、Streaming、Token、Rate Limit。

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Operate and debug the DNS C2 system non-interactively. This skill should be used when Claude needs to launch an exploit, send commands to a compromised session and collect output, diagnose why a payload is not calling home, or inspect C2 server state. Triggers on requests like "run the exploit", "send whoami to the session", "why isn't the payload calling back", "check what sessions are active", or "debug the C2".

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Test Model Context Protocol (MCP) servers and tool-calling systems for security vulnerabilities including tool injection, parameter manipulation, privilege escalation, and data exfiltration through AI agent tool interfaces. Use this skill when assessing MCP server implementations, AI agent tool integrations, or any system that exposes tools to language models. Covers tool confusion attacks, cross-tool exploitation, and MCP server hardening assessment.

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Execute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Use when users need to process ChIP-seq data following ENCODE standards, run peak calling with MACS2, perform IDR analysis, or generate signal tracks. Trigger on: ChIP-seq pipeline, run ChIP-seq, process ChIP-seq, MACS2 peak calling, IDR analysis, ChIP-seq FASTQ processing.

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