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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and Reaction templates, with explicit handling of atom mapping, template extraction (RDKit reaction mining), product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Improve layout, spacing, and visual rhythm. Fixes monotonous grids, inconsistent spacing, and weak visual hierarchy. Use when the user mentions layout feeling off, spacing issues, visual hierarchy, crowded UI, alignment problems, or wanting better composition.

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Find and fix WCAG 2.2 accessibility issues. Two modes — report (sweep a codebase or page, produce a prioritized written report, no edits) and fix (audit→edit→verify loop on a target). Prefers direct-CDP live-DOM auditing; falls back to a browser-MCP composition or HTML-string audits.

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Remove refusal behaviors from open-weight LLMs using OBLITERATUS — mechanistic interpretability techniques (diff-in-means, SVD, whitened SVD, LEACE, SAE decomposition, etc.) to excise guardrails while preserving reasoning. 9 CLI methods, 28 analysis modules, 116 model presets across 5 compute tiers, tournament evaluation, and telemetry-driven recommendations. Use when a user wants to uncensor, abliterate, or remove refusal from an LLM.

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Inspect and analyze codebases using pygount for LOC counting, language breakdown, and code-vs-comment ratios. Use when asked to check lines of code, repo size, language composition, or codebase stats.

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CLI to manage emails via IMAP/SMTP. Use himalaya to list, read, write, reply, forward, search, and organize emails from the terminal. Supports multiple accounts and message composition with MML (MIME Meta Language).

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CLI modernization and hooks system enhancement for claude-flow v3. Implements interactive prompts, command decomposition, enhanced hooks integration, and intelligent workflow automation.

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High-contrast, theatrical design with bold layouts, immersive visuals, and unconventional compositions that command attention.

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Skill for scaffolding, installation, and composition of shadcn-vue components (based on Reka UI v2). Use when you need to install components, understand Vue variants, compose patterns with vee-validate/Zod, or adapt existing components. Stack: Vue 3 + Reka UI v2 + Tailwind CSS.

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Write and refine high-quality user stories — INVEST criteria, "As a X, I want Y, so that Z" format, Gherkin acceptance criteria when applicable, definition of ready, anti-patterns, and a review checklist. Use when creating or reviewing user stories, PRD section 6, backlog items, or acceptance criteria. Do NOT use for technical specs, architecture decisions, or task decomposition.

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Build reusable, composable, and maintainable React/Vue/Angular components following established design patterns like compound components, render props, custom hooks, and HOCs. Use when creating component libraries, implementing component composition, building reusable UI elements, designing prop APIs, managing component state patterns, implementing controlled vs uncontrolled components, creating compound components, using render props or children as functions, building custom hooks, or establishing component architecture standards.

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Provide advisory guidance for the Adobe Dispatcher Apache HTTP Server module and related HTTPD configuration in AEMaaCS cloud workflows only, with public-doc citations and cloud-specific MCP verification plans. Use for conceptual questions such as `statfileslevel`, filter rules, URL decomposition, cache invalidation behavior, rewrite behavior, and security headers.

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Analyze content sequences within a section and provide neutral descriptions for AEM Edge Delivery Services. Invoked per section during page import to identify breaking points between default content and blocks.

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Elite mobile app image-generation skill for creating premium, app-native screen concepts and flows. Designed for iOS, Android, and cross-platform mobile products. Prioritizes clean hierarchy, comfortably readable text, strong multi-screen consistency, controlled color palettes, non-generic creative direction, textured surfaces, image-led composition, tasteful custom iconography, and clean phone mockup framing. By default, screens should be shown inside a subtle premium iPhone or similar phone mockup with a visible frame, while the main focus stays on the app content itself. This skill generates images only. It does not write code.

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Elite frontend image-direction skill for generating premium, conversion-aware website design references. CRITICAL OUTPUT RULE — generate ONE separate horizontal image FOR EVERY section. A landing page with 8 sections produces 8 images. Never compress multiple sections into one image. Enforces composition variety (not always left-text / right-image), background-image freedom, varied CTAs, varied hero scales (giant / mid / mini minimalist), narrative concept spine, second-read moments, and a single consistent palette across all images. Optimized for landing pages, marketing sites, and product comps that developers or coding models can accurately recreate.

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Premium brand-kit image generation skill for creating high-end brand-guidelines boards, logo systems, identity decks, and visual-world presentations. Trained for minimalist, cinematic, editorial, dark-tech, luxury, cultural, security, gaming, developer-tool, and consumer-app brand systems. Optimized for intentional logo concepting, refined composition, sparse typography, strong symbolic meaning, premium mockups, art-directed imagery, and flexible grid layouts.

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Decompose multi-step work into a revisable subgoal plan with stable step IDs, checkpointing, and plan-ahead execution. Load when a task needs explicit planning before action, subgoal decomposition, plan checkpointing, or ReCAP-style plan-ahead execution. Also triggers on "structured plan", "plan with steps", "subgoal graph", "revise the plan", "checkpoint plan", or multi-step tasks where naive one-shot execution would be fragile. Skips trivial single-step tasks. Pairs with dynamic-routing on failure. Distinct from process-decomposer (registry/triage) and problem-to-plan (doc deliverables).

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Route user requests to the right skill, decompose complex work into parallel subagents, and manage project phase transitions. Load when the user asks "what should I do next", "which skill should I use", "orchestrate this", "run the full workflow", "split this into parallel tasks", or when a complex request spans multiple skills. Also triggers on "coordinate agents", "parallel execution", "task decomposition", "agent workflow", "what phase am I in", or when the user gives a broad instruction that requires multiple skills in sequence. This is the project's brain — it decides what runs, when, and whether to parallelise.

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Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-normalized, Pearson-correlated cis matrix with cooltools (eigs_cis), then orients (phases) the compartment eigenvector against a GC or gene-density track so the active (A) sign is not arbitrary. Covers the eigenvector-is-a-choice problem (per-arm view_df to remove the centromere gradient; picking the eigenvector by max correlation with activity, not by eigenvalue), GC phasing with bioframe.frac_gc, resolution choice (100kb-1Mb), saddle plots and saddle_strength for compartmentalization strength, the cohesin-loss-strengthens-compartments result, subcompartments (SNIPER/Calder/dcHiC), and cross-condition compartment switching. Use when calling A/B compartments, computing E1/eigenvectors, phasing the eigenvector, building saddle plots, choosing a compartment resolution, quantifying compartment strength, or comparing compartmentalization across conditions.

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Build enhancer-driven gene regulatory networks (eGRNs) by integrating single-cell RNA-seq and ATAC-seq using SCENIC+, CellOracle base GRNs, Pando, FigR, DIRECT-NET, TRIPOD, and scMEGA. Covers the accessibility-defines-enhancers principle, peak-to-gene linking and its cell-composition confound, the paired-vs-unpaired decision, and TF-region-gene eRegulon triplets. Use when analyzing 10x multiome or paired/unpaired scRNA+scATAC to infer cis-regulatory GRNs. For RNA-only regulons see scenic-regulons; for in silico TF perturbation see perturbation-simulation.

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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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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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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Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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