“tools”的搜索结果

Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.

中文简介正在准备中。当前显示原文说明。

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.

中文简介正在准备中。当前显示原文说明。

Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

中文简介正在准备中。当前显示原文说明。

Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

中文简介正在准备中。当前显示原文说明。

Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

中文简介正在准备中。当前显示原文说明。

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.

中文简介正在准备中。当前显示原文说明。

Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.

中文简介正在准备中。当前显示原文说明。

Audit required bioinformatics command-line tools against Lmod or Environment Modules on Linux HPC clusters, resolve executable and version requirements, and reproducibly deploy missing software through a site-approved EasyBuild, Spack, Bioconda/micromamba, Apptainer, binary, or source-build workflow. Use when Codex must inspect module availability, diagnose a missing or wrong-version bioinformatics tool, install scientific software on Slurm/PBS clusters, publish or validate modulefiles, or produce an auditable and rollback-ready cluster software deployment.

中文简介正在准备中。当前显示原文说明。

Secure the path from an inbound event (webhook, email, SMS, GitHub comment, file, cron) to an agent spawn in the Port Daddy fleet. Use when wiring trigger sources to agents, reviewing the io-wiring registry, adding a trust/permission gate, hardening output sinks (SSRF/path traversal), scoping tools by provenance, or proving the spawn path is safe against prompt-injection → tool-abuse. Encodes ADR-0093 and the red-team threat model. NOT for generic Coast Guard sandboxing (ADR-0050), the macaroon push-grant gate alone (ADR-0053), or non-fleet code.

中文简介正在准备中。当前显示原文说明。

Master of text-based visual communication using ASCII art, Unicode box-drawing, and structured diagram notation. Creates clear, maintainable diagrams for systems, processes, hierarchies, relationships, and psychological structures. Proactively generates diagrams to enhance understanding. Activate on visualization needs, system architecture, process flows, psychological mapping, or when complex concepts would benefit from visual representation. NOT for photo editing, vector graphics, or GUI-based design tools.

中文简介正在准备中。当前显示原文说明。

Expert in developer tool documentation as a product. Activate on: docs site, getting started guide, API reference, developer documentation, Docusaurus, Mintlify, Nextra, ReadMe, migration guide, troubleshooting page, docs information architecture, documentation testing, llms.txt. NOT for: marketing copy (use seo-content-blogging), API design itself (use api-architect), general technical writing (use technical-writer).

中文简介正在准备中。当前显示原文说明。

Send and receive transactional emails with Cloudflare Email Service (Email Sending + Email Routing). Use when building email sending (Workers binding or REST API), email routing, Agents SDK email handling, or integrating email into any app — Workers, Node.js, Python, Go, etc. Also use for email deliverability, SPF/DKIM/DMARC, wrangler email setup, MCP email tools, or when a coding agent needs to send emails. Even for simple requests like "add email to my Worker" — this skill has critical config details.

中文简介正在准备中。当前显示原文说明。

Expert in cluttering -- the lesser-known fluency disorder characterized by rapid/irregular speech rate, excessive disfluencies, and frequent ADHD comorbidity. Covers differential diagnosis from stuttering, assessment protocols, therapy approaches (rate control, self-monitoring, pragmatic awareness), technology-assisted intervention, and AI tools for people who clutter. Activate on 'cluttering', 'rapid speech disorder', 'speech rate too fast', 'speech disfluency not stuttering', 'disorganized speech', 'ADHD speech problems', 'cluttering vs stuttering', 'speech intelligibility', 'mazed speech', 'telescoping words'. NOT for stuttering-only treatment (overlap is common but they are distinct), hearing disorders, or voice disorders (pitch, resonance).

中文简介正在准备中。当前显示原文说明。

Generates shell completion scripts for CLI tools. Parses command structure from help output, commander/yargs configs, or manual specification. Produces completions for bash, zsh, and fish that follow each shell's conventions.

中文简介正在准备中。当前显示原文说明。

Audit whether an enforced-coordination MCP has actually shrunk its ~19 legacy etiquette verbs into the 5 enforced tools — work/act/ask/recall/status — each carrying one denial shape and one transcript event, migrated through a real retirement path (intake-metadata, alias, or doc-history — never a parallel runtime), with zero legacy-verb calls once a body reaches compliance mode C4+. Use when reviewing a broker-collapse migration plan, gating a body's move from advisory (C0-C3) to enforced (C4+) coordination, or verifying IT-018 Broker Collapse compliance. NOT for the inbound trigger→spawn boundary that decides whether an event may spawn an agent at all (use fleet-event-spawn-trust), the capability-token cryptographic mechanism behind a denial (use agentic-zero-trust-security), designing how a swarm of agents invokes and shards work (use swarm-invocation-designer), or auditing an individual PR's mergeability (use agent-pr-authoring).

中文简介正在准备中。当前显示原文说明。

Cooperative vibe coding across machines — real-time collaborative development with humans and AI agents. Covers current tools (Live Share, Code With Me, Zed, Cursor multiplayer, tmux), git-based async patterns, AI agent coordination, and the aspirational future of multi-human multi-agent development. Activate on: "pair programming", "vibe coding together", "collaborative coding", "mob programming", "remote pairing", "code together", "multiplayer coding", "Live Share", "Code With Me", "ensemble programming", "cooperative development". NOT for: building a real-time collaboration ENGINE (use real-time-collaboration-engine), git workflow mechanics (use git-best-practices), single-user AI coding assistance.

中文简介正在准备中。当前显示原文说明。

Design decisions for when and what sounds to use in web apps, mobile apps, and desktop native apps — plus how to create them with AI. Covers UI sound vocabulary (confirms, alerts, transitions, errors), platform conventions (iOS, macOS, Material), creating sounds with AI tools (ElevenLabs, AudioCraft, Stable Audio), Web Audio API for procedural sounds, haptic-audio pairing, and the psychology of satisfying vs. annoying UI sounds. Activate on 'app sounds', 'UI sounds', 'notification sound', 'sound design app', 'earcons', 'sonic branding', 'interaction sounds', 'feedback sounds', 'app audio', 'satisfying sounds'. NOT for professional audio engineering (use sound-engineer), Windows 3.1 retro sounds specifically (use win31-audio-design), music composition (use sound-engineer).

中文简介正在准备中。当前显示原文说明。

Refactor apps so backend owns runtime truth and UI only projects snapshots. Use when tools have split authority. NOT for cosmetic UI work or new features before drift is removed.

中文简介正在准备中。当前显示原文说明。

Designs and audits deterministic, authority-filtered partitions of trust-typed context for already admitted bodies or abstract continuation slots. Use when causal context, obligations, disclosure boundaries, vector-space identity, capacity, and omission proofs must survive partitioning. NOT for spawning or admitting agents, choosing worker count, retrieving arbitrary knowledge, writing successor prompts, or granting tools, leases, identity, or effect authority.

中文简介正在准备中。当前显示原文说明。

Expert in 3D computer vision labeling tools, workflows, and AI-assisted annotation for LiDAR, point clouds, and sensor fusion. Covers SAM4D/Point-SAM, human-in-the-loop architectures, and vertical-specific training strategies. Activate on '3D labeling', 'point cloud annotation', 'LiDAR labeling', 'SAM 3D', 'SAM4D', 'sensor fusion annotation', '3D bounding box', 'semantic segmentation point cloud'. NOT for 2D image labeling (use clip-aware-embeddings), general ML training (use ml-engineer), video annotation without 3D (use computer-vision-pipeline), or VLM prompt engineering (use prompt-engineer).

中文简介正在准备中。当前显示原文说明。

Design low-friction UX, interaction patterns, and comeback loops for AI coding assistant apps, agent consoles, background coding agents, and Port Daddy swarm/operator surfaces. Use when creating flows like prompt-to-diff, context attach, plan/apply/review, checkpoint rollback, background-agent dashboards, visual proof, or multi-agent invocation. NOT for generic landing pages, static dashboards, or implementation-only changes without product flow.

中文简介正在准备中。当前显示原文说明。

Bing Webmaster Tools + IndexNow extension. Microsoft Copilot citations are fed by the Bing index; this skill makes Bing visibility, link data, and IndexNow URL submission first-class.

中文简介正在准备中。当前显示原文说明。

Recipe for creating or changing a floating window. Use when adding a window, deleting, killing or retiring a window or overlay ('kill this panel', 'remove the X window', consolidating X into Y and deleting X), editing a window component, declaring restore or ephemeral behavior, wiring a ?panels= link or the Tools grid, or a window fails to restore after reload. NOT for drag/resize/tray internals (use window-panels) or for opening an overlay (use overlay-system).

中文简介正在准备中。当前显示原文说明。

One-route pattern: public marketing landing plus signed-in workspace. Use when creating or fixing a landing page or a feature's front door, guests see an error, 'make /X work signed out', signed-in users land on a pitch, or ModuleLanding / AuthedWorkspaceCTA. NOT for (public) share viewers or free tools.

中文简介正在准备中。当前显示原文说明。