Claude Code Skills · page 128

Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.

Counts RNA-seq reads overlapping GTF gene features. Takes sorted STAR BAMs plus GTF; outputs a per-gene tab-delimited matrix across samples. Handles strandedness (0/1/2), paired-end, multi-sample batch counting in one command, and outputs assignment statistics. Use Salmon for alignment-free quantification; use featureCounts when STAR BAMs already exist.

GSEA and over-representation analysis (ORA) for RNA-seq and proteomics. Wraps Enrichr for ORA against MSigDB, KEGG, GO, and 200+ databases; runs preranked GSEA on ranked DE gene lists. Outputs enrichment tables and running-score plots. Use after DESeq2 or edgeR for pathway-level interpretation.

Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots. Use for two-group comparisons, multi-factor designs with batch correction, multiple contrasts.

Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM). Builds a k-mer index from transcriptome FASTA, quantifies in minutes. Outputs TPM/count tables (quant.sf) with optional GC- and sequence-bias correction. Integrates with tximeta/tximport for DESeq2/edgeR. Use STAR when a genome-aligned BAM is needed.

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Annotated matrices for single-cell genomics. Stores X with obs/var metadata, layers, embeddings (obsm/varm), graphs (obsp/varp), uns. Use for .h5ad/.zarr I/O, concatenation, scverse integration. For analysis use scanpy; for probabilistic models use scvi-tools.

Automated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores. Use for fast, reference-backed annotation without manual marker inspection.

Query CELLxGENE Census (61M+ cells). Search by cell type/tissue/disease/organism; get AnnData, stream out-of-core, train PyTorch models. For your own data use scanpy; for annotated data use anndata.

Harmony batch correction for scRNA-seq and other omics. Removes batch effects from PCA embeddings while preserving biology. Run after PCA, before UMAP. Scales to millions of cells. Python (harmonypy, scanpy) and R (Seurat).

Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting. Outputs per-method labels, consensus, agreement score. Use when single-method annotation is insufficient or you need ensemble uncertainty for novel states.

scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. Standard scRNA-seq exploration.

Deep generative models for single-cell omics: probabilistic batch correction (scVI), semi-supervised annotation (scANVI), CITE-seq RNA+protein (totalVI), transfer learning (scARCHES), and DE with uncertainty. Unified setup→train→extract API on AnnData. Use harmony-batch-correction for fast linear correction without deep learning; muon for multi-modal MuData workflows.

Decision framework for manual marker-based, automated (CellTypist), and reference-based (popV) cell type annotation in scRNA-seq. Three-tier strategy: Tier 1 manual markers, Tier 2 CellTypist, Tier 3 popV ensemble transfer. Use when planning or troubleshooting annotation.

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.

3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with stick, sphere, cartoon, line, and surface styles; animate trajectories with a frame-delay (interval, ms) control; and animate vibrational normal modes via vibrate() from per-atom dx/dy/dz displacements or from precomputed frames. Output standalone HTML that loads 3Dmol from a CDN, with optional play/pause and speed controls. Use for transition-state imaginary-mode animations, MD or reaction-path playback, docking poses, and orbital/density isosurfaces. For static 2D chemical structure drawings use rdkit-chemdraw-cdxml; for 2D statistical plots use matplotlib or plotly.

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AWS Bedrock AgentCore comprehensive expert for deploying and managing AI agents at scale. Use when working with any AgentCore service including Gateway, Runtime, Memory, Identity, Code Interpreter, Browser, Observability, Agent Registry, or Evaluations. Covers agent deployment, MCP tool integration, credential management, agent discovery, governance workflows, and automated quality assessment. Essential when user mentions AgentCore, agent runtime, agent registry, agent evaluation, MCP gateway, deploy agent, register MCP server, discover agents, evaluate agent quality, agent credentials, or wants to build, deploy, catalog, or monitor AI agents on AWS.

AWS Cloud Development Kit (CDK) expert for building cloud infrastructure with TypeScript/Python. Use when creating CDK stacks, defining CDK constructs, implementing infrastructure as code, or when the user mentions CDK, CloudFormation, IaC, cdk synth, cdk deploy, or wants to define AWS infrastructure programmatically. Covers CDK app structure, construct patterns, stack composition, and deployment workflows.

Configure AWS MCP servers for documentation search and API access. Use when setting up AWS MCP, configuring AWS documentation tools, troubleshooting MCP connectivity, or when user mentions aws-mcp, awsdocs, uvx setup, or MCP server configuration. Covers both Full AWS MCP Server (with uvx + credentials) and lightweight Documentation MCP (no auth required).

AWS cost optimization, monitoring, and operational excellence expert. Use when analyzing AWS bills, estimating costs, setting up CloudWatch alarms, querying logs, auditing CloudTrail activity, or assessing security posture. Essential when user mentions AWS costs, spending, billing, budget, pricing, CloudWatch, observability, monitoring, alerting, CloudTrail, audit, or wants to optimize AWS infrastructure costs and operational efficiency.

AWS serverless and event-driven architecture expert based on Well-Architected Framework. Use when building serverless APIs, Lambda functions, REST APIs, microservices, or async workflows. Covers Lambda with TypeScript/Python, API Gateway (REST/HTTP), DynamoDB, Step Functions, EventBridge, SQS, SNS, and serverless patterns. Essential when user mentions serverless, Lambda, API Gateway, event-driven, async processing, queues, pub/sub, or wants to build scalable serverless applications with AWS best practices.

Generate scroll-stopping viral hook video prompts for Seedance 2.0 on Higgsfield. Use whenever the user wants viral content, TikTok hooks, Instagram Reels openers, YouTube Shorts, attention-grabbing video, scroll-stopper, pattern interrupt, or any short-form video designed to maximize retention and views. Triggers on any mention of viral, hook, scroll-stop, retention, views, engagement, short-form, TikTok, Reels, Shorts.

Generate SaaS product launch and software demo video prompts for Seedance 2.0 on Higgsfield. Use whenever the user wants a product launch video, app demo, software walkthrough, feature showcase, startup promo, tech product reveal, or any SaaS/software marketing video. Triggers on SaaS, app, software, product launch, demo, feature, startup, tech, UI, dashboard, landing page video.

Generate personal brand and founder story video prompts for Seedance 2.0 on Higgsfield. Use for authority content, day-in-the-life, founder story, personal brand building, thought leadership, creator content, lifestyle videos, behind-the-scenes, or any video meant to build a personal brand presence. Triggers on personal brand, founder, creator, authority, lifestyle, behind the scenes, day in the life, thought leader.

Generate online course and coaching program promotional video prompts for Seedance 2.0 on Higgsfield. Use for course trailers, coaching ads, educational content promos, masterclass teasers, webinar promotions, or any educational product video. Triggers on course, coaching, masterclass, webinar, tutorial, education, teaching, training, class, program, academy.

Generate faceless content video prompts for Seedance 2.0 on Higgsfield. Use for faceless YouTube channels, TikTok content without showing face, anonymous creator content, narration-driven videos, stock-footage-style AI content, or any video where the creator doesn't appear on camera. Triggers on faceless, no face, anonymous, narration, stock footage, b-roll, background video, voiceover video.

Generate luxury and premium aesthetic video prompts for Seedance 2.0 on Higgsfield. Use for luxury brand content, premium product showcases, high-end lifestyle, minimalist aesthetic, elegant brand videos, or any content requiring sophisticated visual treatment. Triggers on luxury, premium, high-end, elegant, minimalist, sophisticated, exclusive, refined, designer, couture, bespoke.

Generate before-and-after transformation video prompts for Seedance 2.0 on Higgsfield. Use for transformation reveals, glow-ups, makeovers, renovation reveals, fitness transformations, design before-after, business growth visuals, or any content showing dramatic change. Triggers on before after, transformation, reveal, glow up, makeover, renovation, redesign, progress, results.

Generate customer testimonial and social proof video prompts for Seedance 2.0 on Higgsfield. Use for customer stories, case study videos, review showcases, social proof content, success story videos, or any content featuring customer results and experiences. Triggers on testimonial, review, case study, social proof, customer story, success story, results, feedback, client.

Generate AI avatar and digital persona video prompts for Seedance 2.0 on Higgsfield. Use for virtual spokesperson content, digital twin videos, AI presenter clips, avatar-based marketing, virtual influencer content, or any video featuring a digital/AI-generated character as the main subject. Triggers on avatar, digital persona, virtual presenter, AI character, digital twin, virtual influencer, synthetic media, animated spokesperson.

Generate podcast clip visualization video prompts for Seedance 2.0 on Higgsfield. Use for podcast clip videos, audio-to-visual content, audiogram alternatives, podcast highlight reels, interview clip visuals, or any video that transforms audio content into engaging visual format. Triggers on podcast, audio clip, audiogram, interview clip, sound bite, audio visual, podcast video, episode highlight, podcast clip.

SST v4 (Ion) expert for managing AWS resources as code with the Pulumi-backed framework. Use when writing or editing sst.config.ts, building infra/ modules (sst.aws.Function/Bucket/Dynamo/Cron/Service/Router, sst.Secret, sst.Linkable, raw aws.* Pulumi resources), wiring resource links, scoping IAM, or running sst deploy/dev/diff/remove. Essential when the user mentions SST, sst.config.ts, $config, $transform, $interpolate, sst.aws.*, sst.Secret, Pulumi/Ion, "sst deploy", a failed SST deploy (ConflictException on a resource-type change, "Identifier '__filename' has already been declared", MalformedPolicyDocument on an Output<T>), or wants to scaffold/troubleshoot AWS infrastructure with SST. Also use when a request to "deploy my AWS stack" or "add a Lambda/bucket/table" is made in a repo that already contains an sst.config.ts (using $config) or an sst dependency. Do NOT use when the task is primarily AWS CDK, Terraform, raw CloudFormation, or SAM with no SST present — those have their own tooling.

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Use when reviewing code for security vulnerabilities, implementing authentication/authorization, handling user input, or discussing web application security. Covers OWASP Top 10:2025, ASVS 5.0, LLM Top 10 (2025), and Agentic AI security (2026).

让 OS 在用户离开期间自主推进任务。支持三个子命令：start（启动）、stop（停止）、status（状态查询）。

启动持续工作模式——Leader自动循环领取和执行任务

组织多 Agent 会议全生命周期——创建会议、spawn 真实参与者、推进轮次、签到校验、结束汇总。当需要多方协作做决策、评审方案、辩论分歧、复盘项目、头脑风暴或方案评估时使用本技能。

Participate in AI Team OS meetings with structured discussion rounds

Auto-register as a team member when joining an AI Team OS project

在 AI Team OS 项目里使用 CC 内置 Workflow（ultracode）时，让工作流产出回写 OS 的标准做法。当 Leader 准备调用 Workflow 工具编排子 agent 时使用。

发布 AI Team OS 新版本的完整清单——预检、版本七处锁步、中英双语 CHANGELOG、双份 dist 构建、私有术语扫描、commit/tag、双仓推送、建 GitHub Release 条目并核对 latest 徽章、事后核对。当准备发版、补建漏掉的 Release 条目、或核对已发版本的线上状态时使用。

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Operational knowledge for the daily-brief digest pipeline (this project). RSS/API fetchers, pluggable LLM enrichment (default claude CLI on Max; also anthropic/openai/deepseek/minimax API), trading section, HTML rendering, cross-platform scheduler integration (Windows Task Scheduler / macOS launchd / Linux cron). Load when the user asks about running daily / regenerating sections / debugging a failed run / adding or disabling sources / LLM quota / scheduler / why a tab shows wrong data / why a source failed / switching LLM backend. Always prefer the documented npm commands over re-implementing logic. Diagnose by reading logs/daily-*.log first, then logs/llm-calls.jsonl for LLM-side issues.

Host-side setup, configuration, customization, builds, migration, and troubleshooting for the Aerovato Container CLI. Use when working with Aerovato Container, settings.json, Dockerfile.User, build stages, V2-to-V3 migration, mounts, harnesses, tools, permissions, Docker, or Podman. Do not use it to expose host Container configuration inside managed containers.

Extract .webarchive files (saved from Safari) into plain HTML/assets using the WebArchiveExtractor CLI. Use when the user wants to unarchive, extract, or convert a .webarchive file.

Provides chunking strategies for RAG systems. Generates chunk size recommendations (256-1024 tokens), overlap percentages (10-20%), and semantic boundary detection methods. Validates semantic coherence and evaluates retrieval precision/recall metrics. Use when building retrieval-augmented generation systems, vector databases, or processing large documents.

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Implements document chunking, embedding generation, vector storage, and retrieval pipelines for Retrieval-Augmented Generation systems. Use when building RAG applications, creating document Q&A systems, or integrating AI with knowledge bases.

Provides AWS CloudFormation patterns for Auto Scaling including EC2, ECS, and Lambda. Use when creating Auto Scaling groups, launch configurations, launch templates, scaling policies, lifecycle hooks, and predictive scaling. Covers template structure with Parameters, Outputs, Mappings, Conditions, cross-stack references, and best practices for high availability and cost optimization.

Provides AWS CloudFormation patterns for Amazon Bedrock resources including agents, knowledge bases, data sources, guardrails, prompts, flows, and inference profiles. Use when creating Bedrock agents with action groups, implementing RAG with knowledge bases, configuring vector stores, setting up content moderation guardrails, managing prompts, orchestrating workflows with flows, and configuring inference profiles for model optimization.

Provides AWS CloudFormation patterns for CloudFront distributions, origins (ALB, S3, Lambda@Edge, VPC Origins), CacheBehaviors, Functions, SecurityHeaders, parameters, Outputs and cross-stack references. Use when creating CloudFront distributions with CloudFormation, configuring multiple origins, implementing caching strategies, managing custom domains with ACM, configuring WAF, and optimizing performance.

Provides AWS CloudFormation patterns for CloudWatch monitoring, metrics, alarms, dashboards, logs, and observability. Use when creating CloudWatch metrics, alarms, dashboards, log groups, log subscriptions, anomaly detection, synthesized canaries, Application Signals, and implementing template structure with Parameters, Outputs, Mappings, Conditions, cross-stack references, and CloudWatch best practices for monitoring production infrastructure.

Provides AWS CloudFormation patterns for DynamoDB tables, GSIs, LSIs, auto-scaling, and streams. Use when creating DynamoDB tables with CloudFormation, configuring primary keys, local/global secondary indexes, capacity modes (on-demand/provisioned), point-in-time recovery, encryption, TTL, and implementing template structure with Parameters, Outputs, Mappings, Conditions, cross-stack references.

Provides AWS CloudFormation patterns for EC2 instances, Security Groups, IAM roles, and load balancers. Use when creating EC2 instances, SPOT instances, Security Groups, IAM roles for EC2, Application Load Balancers (ALB), Target Groups, and implementing template structure with Parameters, Outputs, Mappings, Conditions, and cross-stack references.

Provides AWS CloudFormation patterns for ECS clusters, task definitions, services, container definitions, auto scaling, blue/green deployments, CodeDeploy integration, ALB integration, service discovery, monitoring, logging, template structure, parameters, outputs, and cross-stack references. Use when creating ECS clusters with CloudFormation, configuring Fargate and EC2 launch types, implementing blue/green deployments, managing auto scaling, integrating with ALB and NLB, and implementing ECS best practices.

Provides AWS CloudFormation patterns for ElastiCache Redis or Memcached infrastructure, including subnet groups, parameter groups, security controls, and cross-stack outputs. Use when designing cache tiers, high-availability replication groups, encryption settings, or reusable CloudFormation templates for application caching.

Provides AWS CloudFormation patterns for IAM roles, policies, managed policies, permission boundaries, and trust relationships. Use when modeling least-privilege access, cross-account assumptions, service roles, or reusable IAM stacks that other CloudFormation templates consume.

Provides AWS CloudFormation patterns for Lambda functions, layers, API Gateway integration, event sources, cold start optimization, monitoring, logging, template validation, and deployment workflows. Use when creating Lambda functions with CloudFormation, configuring event sources, implementing cold start optimization, managing layers, integrating with API Gateway, and deploying Lambda infrastructure.

Provides AWS CloudFormation patterns for Amazon RDS databases. Use when creating RDS instances (MySQL, PostgreSQL, Aurora), DB clusters, multi-AZ deployments, parameter groups, subnet groups, and implementing template structure with Parameters, Outputs, Mappings, Conditions, and cross-stack references.

Provides AWS CloudFormation patterns for Amazon S3. Use when creating S3 buckets, policies, versioning, lifecycle rules, and implementing template structure with Parameters, Outputs, Mappings, Conditions, and cross-stack references.

Provides AWS CloudFormation patterns for security infrastructure including KMS encryption, Secrets Manager, IAM security, VPC security, ACM certificates, parameter security, outputs, and secure cross-stack references. Use when implementing security best practices, encrypting data, managing secrets, applying least privilege IAM policies, securing VPC configurations, managing TLS/SSL certificates, and implementing defense in depth strategies.

Provides patterns to deploy ECS tasks and services with GitHub Actions CI/CD. Use when building Docker images, pushing to ECR, updating ECS task definitions, deploying ECS services, integrating with CloudFormation stacks, configuring AWS OIDC authentication for GitHub Actions, and implementing production-ready container deployment pipelines. Supports ECS deployments with proper security (OIDC or IAM keys), multi-environment support, blue/green deployments, ECR private repositories with image scanning, and CloudFormation infrastructure updates.

Provides AWS CloudFormation patterns for VPC foundations, including subnets, route tables, internet and NAT gateways, endpoints, and reusable outputs. Use when creating a new network baseline, segmenting public and private workloads, or preparing CloudFormation networking stacks for application deployments.