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Scan an AEM Edge Delivery Services page for WCAG 2.1 AA accessibility violations and generate specific fixes. Identifies missing alt text, heading hierarchy issues, link text problems, color contrast concerns, and EDS-specific accessibility patterns. Use when fixing accessibility issues, preparing for compliance audits, or remediating WCAG violations.
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Audit and update metadata across multiple AEM Edge Delivery Services pages. Scans pages via the query index, identifies missing or inconsistent metadata (titles, descriptions, og tags, robots), and generates a corrected bulk metadata spreadsheet. Use when standardizing metadata across a site, preparing for launch, or fixing SEO issues at scale.
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Use when finishing a feature, fixing a bug, before committing React code, or when the user types `/doctor`, asks to scan, triage, or clean up React diagnostics. Covers lint, accessibility, bundle size, architecture. Includes a regression check and a full local-triage workflow that fetches the canonical playbook.
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Use when finishing a feature, fixing a bug, before committing React code, or when the user asks to scan, triage, or clean up React diagnostics. Covers lint, accessibility, bundle size, architecture, regression checks, and local triage with React Doctor.
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Whole-repo audit for over-engineering. Like ponytail-review, but scans the entire codebase instead of a diff: a ranked list of what to delete, simplify, or replace with stdlib/native equivalents. Use when the user says "audit this codebase", "audit for over-engineering", "what can I delete from this repo", "find bloat", "ponytail-audit", or "/ponytail-audit". One-shot report, does not apply fixes.
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Cross-Reference 進度掃描器 — 自動掃描 assets/scripts/**/*.ts 與 tests/*.ts，比對 cross-ref-code.md B-1 表格，產生進度差異報告。USE FOR: 進度掃描、cross-ref 更新。DO NOT USE FOR: 程式碼編輯、UI layout 調整。
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Extract actionable patterns, architecture decisions, code conventions, and skill-relevant insights from GitHub/GitLab repositories. Assess repo credibility, run the full security scan pipeline, and apply findings to existing skills, new skills, or the current project. Load when the user asks to learn from a repo, extract patterns from a codebase, study a repository, or analyze a repo for reusable techniques. Also triggers on "learn from this repo", "learn from this repository", "what can we learn from this codebase", "extract patterns from this repo", "study this repo".
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Orchestrator for the learn-from suite - auto-detects source type (academic paper, GitHub repo, blog/web article, or in-conversation learnings) and routes to the correct sub-skill for credibility check, security scan, insight extraction, and application. Load when the user says "learn from", "learn from this", "extract insights from", "apply learnings from", "what can we learn from", or provides a URL, file path, or pasted content that should be ingested as knowledge. Single entry point for all learning workflows.
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Execute comprehensive web application security testing using Burp Suite's integrated toolset, including HTTP traffic interception and modification, request analysis and replay, automated vulnerability scanning, and manual testing workflows.
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Meta-skill que orquestra todos os agentes do ecossistema. Scan automatico de skills, match por capacidades, coordenacao de workflows multi-skill e registry management.
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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.
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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.
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Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces. Covers FCS 2.0/3.0/3.1/3.2 internals ($PnE linear-vs-log, $DATATYPE, $SPILLOVER vs SPILL vs $COMP, $TIMESTEP), channel/parameter metadata, the silent linearize/truncate defaults, and R (flowCore, flowWorkspace, CytoML) plus Python (FlowKit, readfcs) readers. Use when loading flow or mass cytometry data, mapping detector channels to antibodies, extracting the event matrix, choosing a reader, or bridging FCS to the scanpy/AnnData ecosystem before preprocessing.
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Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.
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Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.
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Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.
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Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA targets from indirect, integrating CLIP-derived target maps with TargetScan / miRDB / DIANA predictions, applying canonical 7mer-8mer seed matching with 3' UTR context, or recovering miRNA-mRNA chimeras at scale.
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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.
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集群数据管理 Skill —— 涵盖数据使用规范、压缩优化、数据共享（ACL）、文件扫描与清理、文件完整性校验、genozip 基因组压缩等全流程。Use when the user asks about: managing data on the HPC cluster, compressing genomic files (fq/bam/vcf), sharing data between users/groups, scanning for large files or cleaning up disk space, checking file integrity (md5/gzip/bam), using genozip, checking disk quota, or any data lifecycle management task on the NCPGR HPC cluster.
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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.
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Build face recognition systems with InsightFace, ArcFace, enrollment pipelines, HDBSCAN clustering, and privacy-compliant architecture. Activate on: face recognition, face enrollment, face clustering, identity verification, facial search. NOT for: general object detection (computer-vision-pipeline), emotion analysis (ai-engineer).
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Multi-stage Docker build optimizer for minimal, secure production images. Activate on: Dockerfile optimization, multi-stage build, distroless image, container size reduction, Docker security scanning, BuildKit features. NOT for: container orchestration (use kubernetes-manifest-generator), CI/CD pipelines (use github-actions-pipeline-builder), runtime container config (use environment-config-manager).
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Use when optimizing Docker builds with BuildKit, designing multi-stage Dockerfiles, leveraging cache mounts, building multi-arch images, choosing distroless vs alpine, or signing images with cosign. Triggers: docker build slow, layer cache not hitting, npm install / pip install reruns, multi-stage final image bloat, glibc vs musl issues, RUN --mount=type=cache, BUILDKIT_INLINE_CACHE, registry cache exporters, qemu emulation for arm64, COPY ordering for cache. NOT for Docker daemon admin, Kubernetes-specific image policies, container security scanning workflows, or Buildpacks (different paradigm).
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Practical incident-response runbook for a suspected or confirmed ComfyUI / GPU-daemon compromise. Triage, scope, contain, forensic collection, weight-integrity verification, rebuild from clean snapshot, postmortem. NOT for hygiene scans on a healthy box (use supply-chain-defense-for-ml-extensions), and NOT for runtime hardening of a fresh deployment (use gpu-hosted-asset-hardening).
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