“tool calling”的搜索结果

Orchestrates the end-to-end germline short-variant pipeline from FASTQ to a filtered, normalized, benchmarked VCF, chaining QC/trim, BWA-MEM2 alignment, duplicate marking, optional BQSR, calling (bcftools/GATK HaplotypeCaller/DeepVariant/DRAGEN), normalization, site+genotype filtering, annotation, and hap.py/vcfeval benchmarking. Use when deciding the pipeline-wide reference-genome commitment (GRCh38 analysis set vs T2T, ALT/decoy handling), sequencing the steps in the defensible order (normalize BEFORE annotate, filter site- then genotype-level), choosing the calling engine and single-sample vs cohort joint-calling, picking a filtering strategy by cohort size, or benchmarking stratified within GIAB confident regions. Hands off mechanism to the variant-calling and read-alignment component skills; not a re-teach of any single step.

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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046), MeTPeak (HMM over sliding windows; Cui 2016 *Bioinformatics* 32:i378), MACS3 / MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment confirmation via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output formats, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union; cross-caller IDR-equivalent), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody-based methods cannot resolve, and orthogonal-validation routes (miCLIP / GLORI / m6A-SAC-seq / m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set as a whole, reconciling differing peak sets across tools, validating MeRIP peaks against orthogonal single-base methods, interpreting peaks at the 5' end where m6Am contamination is possible, or recommending a multi-tool consensus strategy.

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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046), MeTPeak (HMM over sliding windows; Cui 2016 *Bioinformatics* 32:i378), MACS3 / MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment confirmation via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output formats, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union; cross-caller IDR-equivalent), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody-based methods cannot resolve, and orthogonal-validation routes (miCLIP / GLORI / m6A-SAC-seq / m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set as a whole, reconciling differing peak sets across tools, validating MeRIP peaks against orthogonal single-base methods, interpreting peaks at the 5' end where m6Am contamination is possible, or recommending a multi-tool consensus strategy.

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使用Apple的FoundationModels为iOS 26及以上版本的应用添加端侧语言模型功能，支持文本生成、摘要、数据提取、自定义处理调用和生成过程中的界面更新。

• 离线生成文本和摘要
• 从自然语言中提取表单字段
• 让AI调用应用自定义处理

Guides Python agent development with PydanticAI, covering tool calls and structured outputs checked against defined data types. Explains service injection, provider switching, streaming responses, and tests that run without calling a real language model.

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• Building agents that return validated structured data
• Connecting customer support agents to order data
• Testing agent logic without real model calls

Set up LLM serving with structured responses, including JSON and outputs restricted to specified patterns. Covers reusing shared prompt calculations, tool calling, and multi-turn conversations through SGLang, with examples for server setup and application integration.

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• Extract information into JSON with a defined schema
• Build agents that call tools
• Reuse shared prompts across chat requests

Run builds, tests, and other long commands in the background while continuing other work. Explains how to read new log output, check completion, send input, and stop processes using the available platform controls.

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• Running long builds or tests in the background
• Monitoring development servers and streaming logs
• Taking over an automatically backgrounded command

Plan DNA variant detection workflows by identifying the assay and sample model, then routing to germline, cancer somatic, or molecular-barcode panel skills. It also supports focused local BAM/CRAM checks with variant files, depth summaries, and optional filters.

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• Choosing a workflow for WGS, WES, or DNA panels
• Routing inherited, cancer, and molecular-barcode analyses
• Checking reference genomes and required input files

Build and deploy AI agents on Cloudflare Workers using the Agents SDK. Supports persistent conversation state, live WebSocket connections, scheduled tasks, and tool integration, with guidance for connecting browser or React chat interfaces.

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• Build a chatbot that preserves conversation history
• Connect a live chat interface through WebSockets
• Schedule reminders and recurring background tasks

Build an MCP integration skill using a template that reads server-specific reference notes before calling tools. The Sentry example gathers unresolved errors, groups them by likely root cause, and produces a report with investigation suggestions.

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• Design a skill that integrates with an MCP server
• Document server-specific query pitfalls
• Group Sentry errors by likely root cause

Select technologies for AI and machine learning features in .NET 8+ applications. Get task-specific plans or implementation guidance for structured predictions, text generation, document retrieval, tool-using agents, and running pretrained models locally or in production.

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• Choosing libraries for classification or prediction in .NET
• Adding text generation or summarization to an application
• Designing document retrieval with source-backed AI answers

Customize NVIDIA Nemotron Voice Agent's Generic Pipecat example for healthcare appointment, five-field patient intake, or custom tool-calling workflows without a separate backend.

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Use this skill when creating, editing, or reviewing an Unreal Engine Agent Skill, a named bundle of instructions registered with the unreal-mcp server (distinct from Claude Code's harness skills under `.claude/skills/`). Trigger when the user wants to add or change a skill that the in-editor agent will load. Concrete triggers: 'create a new Agent Skill', 'add a skill for X workflow', 'edit/update this skill', 'review my skill', 'make a Python skill class', 'create a skill UAsset', 'register a skill so Claude picks it up'; writing or editing a `SKILL.md` inside a UE plugin's `Skills/` or `Python/skills/` folder; defining a Python skill class registered with the skill registry; calling `CreateSkill`, `ListSkills`, or `GetSkills` MCP tools; designing a skill's name, description, or instruction body. SKIP for: authoring a toolset (use create-toolset), invoking an existing skill at runtime (use unreal-mcp), editing harness-level Claude Code skills under `.claude/skills/` or `~/.claude/skills/`, or generic uses of the word 'skill'.

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Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM), MeTPeak (HMM over sliding windows), MACS3/MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody methods cannot resolve, and orthogonal validation (miCLIP/GLORI/m6A-SAC-seq/m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set, reconciling differing peak sets across tools, validating MeRIP peaks against single-base methods, interpreting 5' peaks where m6Am contamination is possible, or recommending a consensus strategy.

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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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CloudBase MCP reference. Use when connecting local or remote MCP, calling tools from the shell with mcporter, reading tool schemas, choosing the domestic or international endpoint, setting site, region, cloud mode, or plugin flags, or contributing a fix to the open-source MCP server, skills, or CLI.

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kubectl-mcp-server CLI commands for tool discovery, direct invocation, and diagnostics. Use when exploring available tools, calling tools from command line, or checking server health.

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Use when reviewing, designing, or modifying Java enterprise systems that use AI, LLMs, AI agents, RAG, tool calling, workflow automation, or model-based decision support and need EU AI Act regulatory awareness. This should trigger for requests such as Review a Java AI system for EU AI Act controls; Design governance for an AI agent with enterprise tools; Add human oversight and auditability to LLM workflows; Assess RAG or model-driven decision support before production release. Part of Plinth Toolkit

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Guide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF distributions). Covers detecting raw VCFs via FILTER column and QUAL inspection, QUAL-based filtering with bcftools, Ts/Tv interpretation, and when NOT to filter. Read before any variant-level QC task. See bcftools-variant-manipulation for advanced filters, gatk-variant-calling for caller config, samtools-bam-processing for upstream alignment QC.

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CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.

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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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Register and implement PydanticAI tools with proper context handling, type annotations, and docstrings. Use when adding tool capabilities to agents, implementing function calling, or creating agent actions.

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