Results for “lora”

Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.

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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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Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamada-Kawai, hive plots), edge bundling, community-based coloring, and reproducible seeds using NetworkX, PyVis, igraph, and Cytoscape automation. Use when rendering biological networks for static publication, interactive HTML exploration, or Cytoscape-format export.

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Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen). Use when analyzing categorical outcomes, paired binary endpoints, or testing treatment-outcome independence in confirmatory or exploratory clinical trials.

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Performs logistic regression for clinical trial outcomes (binary, ordinal, multinomial) with marginal-vs-conditional estimand reporting per FDA 2023 covariate adjustment guidance, g-computation/standardisation for marginal effects, modified Poisson for RR, Brant test for proportional odds, Firth penalty for separation, and Hauck-Donner detection. Use when modeling binary or ordinal endpoints in confirmatory or exploratory clinical trials.

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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

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Refute-before-prove research discipline: automated counterexample sweeps before any formalization, meter-integrity audits for information-bound experiments, mutation-tested model checkers, pre-registered commit-or-cut gates for speculative directions, wrong-turn reporting, and numeric-claim provenance. Use when validating any new theorem, bound, equilibrium, or security claim; when building or trusting a checker, simulator, or experiment; or when deciding whether a speculative research direction lives or dies. NOT for exploratory brainstorming, product prioritization, writing style, or literature review.

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Facilitate idea generation sessions that actually produce diverse, useful options instead of degenerating into the first plausible answer. Use for product ideation, feature exploration, problem-reframing, naming, design alternatives, strategic option-generation, or any task where the failure mode is "we picked the obvious thing too fast." Covers solo and group sessions, divergence/convergence discipline, technique selection (SCAMPER, Crazy Eights, How Might We, 6-3-5 Brainwriting, Reverse Brainstorming, Worst Possible Idea, Random Stimulus), facilitation moves for handling dominant voices and groupthink, and structured convergence to a shortlist with rationale. Outputs a session artifact with options generated, evaluation, shortlist, and the rejected-but-interesting list.

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Create polished, validated architecture, workflow, sequence, data-flow, and lifecycle/state diagrams as explorable standalone HTML with inline SVG, dark/light themes, optional trace motion, and PNG/JPEG/WebP/SVG/WebM export. Accept plain-language requirements or pasted Mermaid flowchart, sequenceDiagram, and stateDiagram input; inspect repository evidence when the diagram must reflect real code. Use when the user asks to visualize system architecture, infrastructure, cloud/security/network topology, technical workflows, API call sequences, request lifecycles, data pipelines, ETL/ELT, data lineage, state machines, or to convert/beautify Mermaid.

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Create algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use when users request generative art, algorithmic art, flow fields, or particle systems. Create original works rather than copying existing artists.

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Abductive analysis for qualitative interview data following Timmermans & Tavory. Guides you through theory-first analysis that recognizes anomalies and generates novel theoretical insights through systematic puzzle exploration.

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Hypothesis-Test Loops via REPL for Exploratory Abductive Inference with Gay.jl colors

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Create stunning, animation-rich HTML presentations from scratch or by converting PowerPoint files. Use when the user wants to build a presentation, convert a PPT/PPTX to web, or create slides for a talk/pitch. Helps non-designers discover their aesthetic through visual exploration rather than abstract choices.

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Systematically explore and test a web application to find bugs, UX issues, and other problems. Use when asked to "dogfood", "QA", "exploratory test", "find issues", "bug hunt", "test this app/site/platform", or review the quality of a web application. Produces a structured report with full reproduction evidence -- step-by-step screenshots, repro videos, and detailed repro steps for every issue -- so findings can be handed directly to the responsible teams.

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Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright violations.

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Website exploration for testing using Playwright MCP

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Throwaway HTML mockups: 2-3 design variants to compare.

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Throwaway experiments to validate an idea before build.

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Iterative Python via live Jupyter kernel (hamelnb).

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Phase 1 of the Forge pipeline. Gather real context from the codebase, answer everything the code can answer through exploration, then grill the user one question at a time (with a recommended answer) for only what code cannot answer, and write a research document. Use when starting /forge-research or the research step of /forgemaster, or when the user wants a research-first investigation before planning a feature.

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Configure or diagnose project context, rules files, context packs, or documented context degradation when explicitly requested; do not trigger automatically at session start, task switching, ordinary repository exploration, implementation, or completion.

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Use when a study needs a preregistration or a frozen analysis plan, when confirmatory and exploratory analyses must be separated, or when every deviation from the registered plan must be logged before the result is reported.

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IoT and embedded device security testing methodology. Covers hardware reconnaissance (UART, JTAG, SWD, SPI flash, I2C EEPROM, eMMC chip-off), firmware acquisition (vendor portals, OTA capture, flash dump, binwalk extraction), firmware analysis (filesystem mounting, binary triage, hardcoded secrets, default credential discovery), bootloader attacks (U-Boot console, secure-boot bypass, fault injection), runtime attacks on embedded Linux/RTOS (busybox CVEs, MTD writes, /dev/mem), wireless protocol attacks (Zigbee, BLE, Z-Wave, LoRaWAN, Thread/Matter, sub-GHz), MQTT/CoAP/Modbus/BACnet/OPC-UA exploitation, mobile companion app analysis, cloud-IoT API abuse, and side-channel/glitching basics. Use for IoT pentest, smart-home assessment, ICS/OT testing, or embedded vulnerability research.

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Microsoft 365 / Entra ID red-team attack chain — current 2026 reality. AADSTS code reference, user enumeration vectors (with hardening status), Smart Lockout math, Conditional Access bypass options, ROPC + SAML SSO browser flow, Burp/Playwright templates. Built from authorized red-team work where ROPC spray surfaced pre-existing lockouts and CA-blocked credentials, plus real-time external attacker activity correlation. Use for any M365/Entra credential attack, password spray, user enumeration, CA-bypass exploration, or active-attacker-detection scenario.

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