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Detects TAD boundaries from balanced Hi-C contact matrices via the diamond-window insulation score (cooltools insulation) and HiCExplorer hicFindTADs, returning a continuous log2 insulation track, valley-prominence boundary_strength, and Li/Otsu-thresholded is_boundary flags across a list of window sizes. Covers the multi-scale window sweep (sub-TAD to compartment-domain), why the boundary is reproducible but the domain partition is not, cross-condition comparison via differential SCORE not differential partition, and the insulation-vs-compartment orthogonality. Use when calling TADs or domain boundaries, computing insulation scores, choosing a window size, ranking boundary strength, comparing boundaries across conditions, or annotating CTCF-backed boundaries; route domain rendering to hic-visualization and boundary-feature overlap to genome-intervals.

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Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedtools genomecov, deepTools bamCoverage/bamCompare/bigwigCompare, bedtools unionbedg, and UCSC bedGraphToBigWig. Covers why a raw coverage bedGraph is not comparable across samples until normalized, the CPM/RPKM/BPM/RPGC normalization menu and the conserved-total assumption that makes them wrong under a global perturbation, the strict sorted-non-overlapping-chrom.sizes bedGraphToBigWig contract that silently corrupts a bigWig, effective-genome-size selection, and bin-size aliasing. Use when building or normalizing a coverage/signal track from a BAM, comparing tracks across samples or conditions, converting bedGraph to a browser-ready bigWig, or diagnosing a track that looks plausible but reports wrong heights.

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Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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Compare gene co-expression and regulatory networks between biological conditions to find rewired relationships using DiffCorr, DiffCoEx, DINGO/iDINGO, and CoDiNA. Covers the differential-connectivity-is-not-differential-expression distinction, the pairwise multiple-testing explosion, marginal vs partial (direct) rewiring, and the underpowered-rewiring failure mode. Use when comparing co-expression networks between disease vs control, treatment, or developmental stages, or finding hub genes that rewire without changing mean expression. For single-condition modules see coexpression-networks; for differential expression of means see differential-expression/de-results.

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Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring. Covers the motif-pruning-as-directionality principle, regulon specificity scoring, run-to-run stability, and database/species matching. Use when identifying TF regulons, scoring TF activity per cell, finding master regulators of cell identity, or comparing regulon activity across conditions. For enhancer-driven multiomic GRNs see multiomics-grn; for bulk inference and VIPER protein-activity see grn-inference.

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

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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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Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers between conditions, identifying master transcription factor networks, or predicting BET-inhibitor responsiveness.

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Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning 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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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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Use when the user mentions flaky tests, tests that pass locally but fail in CI, race conditions in tests, or needs to diagnose WHY a specific test fails.

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End-to-end finite element analysis in MATLAB PDE Toolbox — geometry creation, model setup, solve, and post-processing in one skill. Use when building geometry from primitives or file import, setting up femodel with BCs/loads/materials, solving thermal/structural/EM problems, and extracting or visualizing results. Covers fegeometry, multicuboid, multicylinder, multisphere, decsg, boolean ops, mesh generation, femodel, all AnalysisTypes (thermalSteady, thermalTransient, structuralStatic, structuralTransient, structuralModal, structuralFrequency, electrostatic, magnetostatic, dcConduction, harmonic EM), materialProperties, faceBC, faceLoad, cellLoad, vertexLoad, solve, interpolation, von Mises stress, principal stress, reaction forces, heat flux, pdeplot3D visualization. Triggers on: PDE Toolbox, finite element, FEA, thermal analysis, structural analysis, electromagnetic analysis, femodel, mesh, boundary conditions, stress, displacement, heat transfer, post-processing.

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Programmatically author RoadRunner scenarios from MATLAB using roadrunnerAPI. Use when adding actors, creating routes, building scenario logic (phases, conditions, actions), placing vehicles/pedestrians, defining cut-in/crossing/ follow scenarios, or any programmatic scenario creation in RoadRunner. Triggers on: roadrunnerAPI, scenario authoring, add actor, create route, phase logic, cut-in scenario, pedestrian crossing, scenario from MATLAB.

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E-commerce email marketing system builder. Creates complete email automation flows with full copywriting, subject lines, ESP setup instructions, segmentation rules, and annual campaign calendars. Generates copy-paste-ready email sequences for Klaviyo, Omnisend, Mailchimp, or any ESP. Covers welcome series, cart abandonment, browse abandonment, post-purchase, review requests, cross-sell, win-back, VIP/loyalty, replenishment, and sunset flows. Includes A/B test subject line variants, send timing, trigger conditions, branching logic, and seasonal campaign calendar. No API key required. Use when: (1) setting up email marketing for an e-commerce store, (2) writing email sequences and flows, (3) planning seasonal email campaigns.

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Review, run, debug, and verify approved Python modeling code against its code plan, data contract, method decision, risk conditions, and experiment outputs, saving one compact JSON review.

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Build, transform, audit, and migrate prompts for GPT-5.6 Sol using outcome-first contracts, explicit success criteria, evidence and tool rules, approval boundaries, output requirements, and stop conditions. Use when someone asks for a GPT-5.6 prompt, wants an existing prompt optimized for GPT-5.6, or needs a prompt stack adapted from an older model.

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Pre-landing PR review with two-pass checklist. Pass 1 critical: SQL safety, race conditions, LLM trust boundaries, enum completeness. Pass 2 informational: side effects, magic numbers, dead code, test gaps. Adversarial review auto-scaled by diff size. Scope drift detection.

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Determines whether a specific AI-agent action, output, recommendation, or proposed commitment remains admissible for execution or institutional reliance under current authority, delegated scope, evidence, facts, policy, risk, escalation, and revocation conditions. Use this Skill before an enterprise or regulated AI agent executes, updates records, triggers workflows, communicates externally, or before an institution relies on an agentic output in a way that creates consequence.

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Performs a legal compliance audit for a Moroccan e-commerce website, focused on personal data protection (Law 09-08) and consumer contract disclosures/obligations (Law 31-08). Use this skill when a user asks to audit, check, or assess the legal compliance of an e-commerce website operating in Morocco — presence and validity of Terms & Conditions, privacy policy, CNDP declaration, mandatory disclosures, right of withdrawal, consent banner. Out of scope: compliance for other countries, Meta/Google advertising compliance (covered by another skill), definitive legal advice (results are a starting point for professional review, not legal advice).

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Use this skill when asked about Icelandic employment law, labour relations, workplace rights, or collective agreements. Triggers on questions about hiring, termination, working conditions, parental leave, trade unions, collective bargaining, workplace safety, or the Félagsdómur labour court in Iceland.

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Audits a legal document against legal design principles. Scores the document on six pillars: language patterns (bureaucratese, archaisms, passive voice, nominalization), readability (Flesch Reading Ease and language-specific equivalents), structure and navigation, hidden conditions (material obligations buried away from their headings), statutory duplication (restating the law instead of citing it), and visual hierarchy where layout is available. Assessment-only; does not rewrite the document. Works on English, French, and German documents, inferring the applicable jurisdiction from the document's language and textual signals: governing-law clause, statute citations, party addresses. Use when a user shares a legal document (contract, NDA, T&C, privacy policy, internal policy) asking how good the drafting is from a legal design perspective, whether it is readable, whether it contains buried clauses or restates the law, or how it scores on Flesch / LIX / Amstad / Kandel-Moles readability metrics.

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