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Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.

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SCIP optimization with PySCIPOpt. Use when facing an optimization problem with an objective, hard constraints, soft penalties, integer decisions, routing, assignment, scheduling, allocation, packing, capacity, inventory, or service-level rules. Prefer modeling and solving the problem with PySCIPOpt when it is available.

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Translate logistics and operations rules into optimization variables and constraints. Use when an operations problem describes vehicles, routes, depots, pickups, dropoffs, inventory, capacity, assignments, time windows, service targets, penalties, resource limits, or other business rules that need to become an optimization model.

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Prepare and manage durable MEX team handoffs in git-native project memory. Use when the user asks to hand work to a person or team, prepare an end-of-session handoff, save what the next engineer needs, create a MEX Relay, take or close a Relay, or invokes /mex-relay or $mex-relay. Keywords: mex, project memory, relay, handoff, team memory, Claude Code, Codex. Treat Relay as a memory baton, not chat, notifications, task assignment, issue tracking, or a Jira replacement; do not activate for ordinary status messages that are not durable handoffs.

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Prepare and manage durable MEX team handoffs. Use when the user asks to hand work to a person or team, prepare an end-of-session handoff, save what the next engineer needs, create a MEX Relay, take or close a Relay, or explicitly invokes /mex-relay or $mex-relay. Treat Relay as a memory and context baton, not chat, notifications, task assignment, issue tracking, or a Jira replacement; do not activate for ordinary status messages that are not durable handoffs.

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Scaffold a graded problem set with sections, problems, worked solutions, and short "why this matters" explainers across analytical, empirical, and coding types. Use when user says "make a problem set on X", "scaffold exercises for this lecture", "create practice problems", "generate homework with a solution key", "build a graded assignment on topic Y". Emits a clean student set plus a separate solution key — NOT for grading submissions or auto-checking student answers.

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Build, deploy, evaluate, optimize, fine-tune, and manage Microsoft Foundry agents, models, and resources end to end. USE FOR: foundry, azd ai agent, azd provision/deploy, hosted agent scaffold/develop/run/deploy/troubleshoot, prompt agent create, create agent, update agent, add tool to agent, invoke agent, agent.yaml, agent insights, pull agent insights, evaluate agent, batch eval, continuous eval, continuous monitoring, agent CI/CD, optimize prompt, improve prompt, prompt optimizer, optimize agent instructions, Agent Optimizer scaffold, dataset curation from traces, deploy model, model fine-tuning (SFT/DPO/RFT), Foundry project, RBAC, role assignment, permissions, quota, capacity, region, deployment failure, AI Services, create Foundry resource, knowledge index, customize deployment, onboard, availability, training-data, grader, distillation, large file upload. DO NOT USE FOR: Azure Functions, App Service, general Azure deploy (use azure-deploy), general Azure prep (use azure-prepare).

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Coordinates parallel investigation threads to simultaneously explore multiple hypotheses or root causes across different system areas. Use when debugging production incidents, slow API performance, multi-system integration failures, or complex bugs where the root cause is unclear and multiple plausible theories exist; when serial troubleshooting is too slow; or when multiple investigators can divide root-cause analysis work. Provides structured phases for problem decomposition, thread assignment, sync points with Continue/Pivot/Converge decisions, and final report synthesis.

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Governs Microsoft Fabric OneLake catalog health, protection, and trust through Fabric Admin, Core, and Power BI REST APIs. Use for tenant or owner-scoped audits and guarded remediation of domains, workspace assignment, capacity, labels, tags, descriptions, refresh, and item identity. Catalog item discovery belongs to search-consumption-cli.

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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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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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Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity matrices for clustering, classifying archaea, evaluating MAG (metagenome-assembled genome) species assignment, applying skani for fast metagenomic ANI screening, or reconciling 16S rRNA-based taxonomy with whole-genome ANI.

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Run explicitly requested Autoprompt work with task routing, owned assignments, independent checks, and bounded recovery.

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Break down Claude Code usage by model family (Opus / Sonnet / Haiku) from the Agent Monitor dashboard — each family's share of tokens, share of cost, and the spots where an expensive model is doing cheap work. Pulls per-model token and cost splits from /api/pricing/cost, current rates from /api/pricing, fleet token totals from /api/analytics, and per-session model assignment from /api/sessions. Use when deciding model routing or whether to downshift work to a cheaper tier.

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Running experiments out of the data warehouse instead of via dedicated experiment platforms. SQL-based assignment, exposure logging discipline, metric definitions in dbt models, statistical analysis in SQL or Python, variance reduction with CUPED, sequential testing, and the operational tradeoffs vs platforms like Statsig and Optimizely. Triggers on warehouse-native experimentation, run experiments in BigQuery, run experiments in Snowflake, dbt experiments, SQL t-test, CUPED variance reduction, exposure log, sample ratio mismatch, sequential testing, mSPRT, doubly robust estimation, build vs buy experimentation. Also triggers when the team is choosing between platform and warehouse, building warehouse-native experiment infrastructure, auditing one, or running an experiment with a custom metric the platform cannot handle.

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Manage the agency SOP library: templates, assignments, compliance. "create an SOP for blog publishing"

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Convert agreed scope into a structured matter plan — phases, workstreams, milestones, dependencies, owner assignments, and matter setup decisions. Use when planning a new matter, running a kickoff, building a workstream plan, structuring phases, setting up task codes, or producing a plan to drive status reporting. Trigger on: 'build a plan', 'matter plan', 'project plan', 'what are the phases', 'workstream plan', 'how do we sequence this', 'who owns what', 'task codes', 'matter setup', 'workstream plan', 'matter plan', 'rolling wave', 'plan the next phase', 'what comes first', 'kickoff agenda'.

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Maps the full set of legal obligations for the EU AI Act based on role + risk tier, producing an actionable compliance matrix with RACI assignments and implementation priorities. This skill should be used when the user asks to "map AI Act obligations", "check what we need to do under the AI Act", "create a compliance checklist", "check deployer obligations", "assess provider duties", or mentions Art. 26, Art. 16-17, AI literacy Art. 4, DPIA, fundamental rights assessment, or "Pflichtenkatalog" under the AI Act.

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A drafting-and-review copilot for a founders' / co-founders' agreement — the terms fixing equity, vesting, IP, roles, control, deadlock, and departure between cofounders. Jurisdiction-agnostic, anchored on the Delaware C-corp default. Two modes: DRAFT (intake → equity & vesting → clauses → blocker triage → pre-signature check) and REVIEW (audit an existing agreement against an 18-clause checklist and red-flag scan). It handles the highest-dispute terms first-class: the equity split as documented reasoning (not a fake calculator), reverse vesting and the 83(b) clock, present-tense IP assignment (the Stanford v. Roche trap), leaver buyback and dead equity, and the deadlock clause most tools omit. It drafts for the venture, never one founder against another. Not legal advice.

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Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and

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Universal LaTeX document skill: create, compile, and convert any document to professional PDF with PNG previews. Supports resumes, reports, cover letters, invoices, academic papers, theses/dissertations, academic CVs, presentations (Beamer), scientific posters, formal letters, exams/quizzes, books, cheat sheets, reference cards, exam formula sheets, fillable PDF forms (hyperref form fields), conditional content (etoolbox toggles), mail merge from CSV/JSON (Jinja2 templates), version diffing (latexdiff), charts (pgfplots + matplotlib), tables (booktabs + CSV import), images (TikZ), Mermaid diagrams, AI-generated images, watermarks, landscape pages, bibliography/citations (BibTeX/biblatex), multi-language/CJK (auto XeLaTeX), algorithms/pseudocode, colored boxes (tcolorbox), SI units (siunitx), Pandoc format conversion (Markdown/DOCX/HTML ↔ LaTeX), and PDF-to-LaTeX conversion of handwritten or printed documents (math, business, legal, general). Compile script supports pdflatex, xelatex, lualatex with auto-detection, latexmk backend, texfot log filtering, PDF/A output, and verbosity control (--verbose/--quiet). Empirically optimized scaling: single agent 1-10 pages, split 11-20, batch-7 pipeline 21+. Use when user asks to: (1) create a resume/CV/cover letter, (2) write a LaTeX document, (3) create PDF with tables/charts/images, (4) compile a .tex file, (5) make a report/invoice/presentation, (6) anything involving LaTeX or pdflatex, (7) convert/OCR a PDF to LaTeX, (8) convert handwritten notes, (9) create charts/graphs/diagrams, (10) create slides, (11) write a thesis or dissertation, (12) create an academic CV, (13) create a poster, (14) create an exam/quiz, (15) create a book, (16) convert between document formats (Markdown, DOCX, HTML to/from LaTeX), (17) generate Mermaid diagrams for LaTeX, (18) create a formal business letter, (19) create a cheat sheet or reference card, (20) create an exam formula sheet or crib sheet, (21) condense lecture notes/PDFs into a cheat sheet, (22) create a fillable PDF form with text fields/checkboxes/dropdowns, (23) create a document with conditional content/toggles (show/hide sections), (24) generate batch/mail-merge documents from CSV/JSON data, (25) create a version diff PDF (latexdiff) highlighting changes between documents, (26) create a homework or assignment submission with problems and solutions, (27) create a lab report with data tables, graphs, and error analysis, (28) encrypt or password-protect a PDF, (29) merge multiple PDFs into one, (30) optimize/compress a PDF for web or email, (31) lint or check a LaTeX document for common issues, (32) count words in a LaTeX document, (33) analyze document statistics (figures, tables, citations), (34) fetch BibTeX from a DOI, (35) convert a Graphviz .dot file to PDF/PNG, (36) convert a PlantUML .puml file to PDF/PNG, (37) create a one-pager/fact sheet/executive summary, (38) create a datasheet or product specification sheet, (39) extract pages from a PDF (page ranges, odd/even), (40) check LaTeX package availability before compiling, (41) analyze citations and cross-reference with .bib files, (42) debug LaTeX compilation errors, (43) make a document accessible (PDF/A, tagged PDF), (44) create lecture notes or course handouts, (45) fill an existing PDF form (fillable fields or non-fillable with annotations), (46) extract text or tables from a PDF (pdfplumber, pypdf), (47) OCR a scanned PDF to text (pytesseract), (48) create a PDF programmatically with reportlab (Canvas, Platypus), (49) rotate or crop PDF pages (pypdf), (50) add a watermark to an existing PDF, (51) extract metadata from a PDF (title, author, subject).

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Expert knowledge for Azure Role-based access control development including troubleshooting, best practices, decision making, limits & quotas, security, configuration, and integrations & coding patterns. Use when defining custom/built-in roles, ABAC conditions, deny assignments, PIM, or ARM/Bicep-based role automation, and other Azure Role-based access control related development tasks. Not for Azure Policy (use azure-policy), Azure Security (use azure-security), Azure Resource Manager (use azure-resource-manager), Azure Portal (use azure-portal).

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Expert knowledge for Azure Network Function Manager development including security, and configuration. Use when setting up NF Manager prerequisites, resource groups, managed identities, role assignments, or secure NF access, and other Azure Network Function Manager related development tasks. Not for Azure Firewall Manager (use azure-firewall-manager), Azure Virtual Network Manager (use azure-virtual-network-manager), Azure Virtual Network (use azure-virtual-network), Azure Virtual WAN (use azure-virtual-wan).

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Use when briefing or managing an EXTERNAL agency, freelancer, or production vendor — scope of work, deliverable specs, revision rounds, approval process, USD payment milestones, IP assignment and confidentiality terms, communication rules, and a post-project vendor scorecard. Trigger on 'brief an agency', 'hire a freelancer', 'scope of work', 'the agency is not delivering', 'onboard a new vendor', 'we keep paying for work we have to redo'. Also use when the user is about to sign a supplier with nothing written down. Not for — briefing an internal team member, see `64-team-brief-global`; the campaign brief itself, see `02-campaign-brief-global`; the asset list the vendor produces, see `41-campaign-asset-list-global`.

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