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Target a specific Google Chrome user profile for browser automation via CDP. Discovers installed profiles from the Chrome Local State file, launches Chrome with the requested profile attached to a debug port, and connects agent-browser via `agent-browser connect <port>`. Use when "automate using my Work/Personal Chrome", "open site with my saved session", or "use Chrome profile named <name>". NOT for headless scraping without an existing user profile (use mk:agent-browser directly); NOT for importing cookies only (use agent-browser --auto-connect state save).

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Use when the user asks about website analytics, traffic, visitors, page views, referrers, conversions, goals, or mentions "fusionaly". Answers from a self-hosted Fusionaly instance through its MCP tools (or its SQL API), in plain English with numbers.

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Use when user asks about website analytics, traffic, visitors, page views, referrers, or mentions "fusionaly". Queries Fusionaly analytics via SQL API.

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Create aesthetically beautiful interfaces following proven design principles. Use when building UI/UX, analyzing designs from inspiration sites, generating design images with ai-multimodal, implementing visual hierarchy and color theory, adding micro-interactions, or creating design documentation. Includes workflows for capturing and analyzing inspiration screenshots with chrome-devtools and ai-multimodal, iterative design image generation until aesthetic standards are met, and comprehensive design system guidance covering BEAUTIFUL (aesthetic principles), RIGHT (functionality/accessibility), SATISFYING (micro-interactions), and PEAK (storytelling) stages. Integrates with chrome-devtools, ai-multimodal, media-processing, ui-styling, and web-frameworks skills.

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Process multimedia files with FFmpeg (video/audio encoding, conversion, streaming, filtering, hardware acceleration) and ImageMagick (image manipulation, format conversion, batch processing, effects, composition). Use when converting media formats, encoding videos with specific codecs (H.264, H.265, VP9), resizing/cropping images, extracting audio from video, applying filters and effects, optimizing file sizes, creating streaming manifests (HLS/DASH), generating thumbnails, batch processing images, creating composite images, or implementing media processing pipelines. Supports 100+ formats, hardware acceleration (NVENC, QSV), and complex filtergraphs.

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Python Invoke task automation for DTX website. This skill should be used when running repo commands, backend tests via Docker, database migrations, updating invoke tasks, Docker operations, or workflow automation. Supports dev/test/prod environments with run, exec, up, down commands. References docs/development/invoke-tasks.md for complete command reference.

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Build a LiveAvatar integration end-to-end — assesses the user's existing stack, recommends the optimal path, and guides implementation. Use when: (1) Building a new LiveAvatar integration, (2) Adding a real-time avatar to an app or site, (3) Connecting LiveAvatar to an existing AI pipeline, (4) User mentions LiveAvatar, real-time avatar, interactive avatar, conversational avatar, or lip-sync avatar, (5) Deciding between Embed, FULL Mode, and LITE Mode, (6) Migrating from HeyGen Interactive Avatar to LiveAvatar.

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Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-element bead normalization of instrument sensitivity drift (CATALYST normCytof, premessa), and reference-anchor cross-batch normalization (CytoNorm, per-cluster quantile splines). Covers the distinction between within-run drift correction and between-batch correction, the mandatory anchor/reference sample, why normalization is per-cluster with many quantiles, and the over-correction risk. Use when correcting CyTOF signal drift, harmonizing multi-batch or multi-site studies, or deciding whether to normalize data versus model batch in the design.

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Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-analysis).

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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.

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Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/amplicon consensus with iVar. Use when reconstructing a sample-specific reference or haplotype, deciding -H haplotype vs IUPAC vs all-ALT projection, masking no-coverage sites so a consensus does not manufacture false reference calls, or setting iVar min-depth/min-frequency policy for surveillance genomes.

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Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), TRIBE/HyperTRIBE (ADAR-RBP, A-to-I editing), DART-seq (APOBEC1-YTH for m6A), or Bullseye/SAILOR edit-site detection pipelines. Use when antibody is unavailable or specificity is doubtful, when single-cell RBP profiling is needed (scSTAMP), or when in vivo RBP profiling without UV is preferred.

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Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

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Interactive Archon integration for knowledge base and project management via REST API. On first use, asks for Archon host URL. Use when searching documentation, managing projects/tasks, or querying indexed knowledge. Provides RAG-powered semantic search, website crawling, document upload, hierarchical project/task management, and document versioning. Always try Archon first for external documentation and knowledge retrieval before using other sources.

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Given an article DOI or PubMed ID, discover and download the genomics data files deposited by the authors (VCF, FASTA, H5AD, CSV, JSON, BAM, etc.) from public repositories such as GEO, ENA, Zenodo, Figshare, Dryad, and OSF.

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On-demand "what's new" generator. Main context (which knows the impending change) writes keepachangelog-style entries to a fragment file at `.claude/state/whatsnew/<slug>.json` (gitignored, transient). An optional per-project `project.json → whatsnew.route_workflow` names a routing workflow that consumes the fragment and renders it wherever the project wants (a site page, a release body, a docs page). Not a workflow phase — it never blocks a commit, and it never writes `CHANGELOG.md` (that file is owned solely by semantic-release in CI).

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Derive an execution roadmap from a project's vision/spec docs by first principles, then diff that fresh derivation against the existing roadmap to prove the task ORDER is correct. Use this whenever the user wants to review, validate, re-derive, or sanity-check an execution roadmap or delivery plan; asks whether the tasks/epics are "in the right order"; suspects a task is scheduled before its prerequisite (a producer-after-consumer / dependency-inversion error like "OpenAPI after the web client that consumes it", OR a cross-cutting inherited default like observability/auth/tenancy scheduled after the feature work that inherits it — a seam-after-consumer error); wants to find missing tasks, circular dependencies, or over-fragmented epics; or wants to compact a plan to raise velocity. Also trigger on "review the roadmap", "re-derive the plan from the spec", "is this the right build order", "check the dependency graph of our epics", "which task should come first". It reads the vision + spec corpus, decomposes actors → use-cases → modules → epics → typed tasks, identifies cross-cutting inherited-default seams, builds a real dependency graph with hard + soft (seam) edges (deterministic helper), breaks cycles, topologically orders, compacts, and emits a derived roadmap PLUS a delta report against the current one — it never blindly overwrites a hand-crafted roadmap.

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Use when the user wants to design, redesign, shape, critique, audit, polish, clarify, distill, harden, optimize, adapt, animate, colorize, extract, or otherwise improve a frontend interface. Covers websites, landing pages, dashboards, product UI, app shells, components, forms, settings, onboarding, and empty states. Handles UX review, visual hierarchy, information architecture, cognitive load, accessibility, performance, responsive behavior, theming, anti-patterns, typography, fonts, spacing, layout, alignment, color, motion, micro-interactions, UX copy, error states, edge cases, i18n, and reusable design systems or tokens. Also use for bland designs that need to become bolder or more delightful, loud designs that should become quieter, live browser iteration on UI elements, or ambitious visual effects that should feel technically extraordinary. Not for backend-only or non-UI tasks.

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Drift check between the baseline implementation on disk and the claims in `docs/init/seed.md` + cross-references in CLAUDE.md, README.md, and the rendered docs site. Verifies hook/agent/skill/command names + counts, settings.json wiring, project.json key presence, .mcp.json servers, vendored license files, and helper script presence. Exit 0 PASS / 1 FAIL — suitable for CI. Read-only; safe to invoke any time.

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。