Results for “linear”

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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Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 detects enrichment), and BF-to-FDR calibration (BF >6 ≈ FDR 0.05 from Hart 2017). Use when classifying essential vs non-essential genes, calibrating BAGEL2 thresholds against PR curves, identifying tumor suppressors alongside essentials, comparing BAGEL2 hits to MAGeCK / drugZ, or generating publication-quality essentiality calls.

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Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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Validates typed DAG dependency declarations, returns Kahn linear extensions or generations and residual cycle witnesses, and identifies changed consumers for revalidation. NOT for constructing graphs, scheduling resource capacity, granting effects, or executing nodes.

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Parses complex problems into candidate DAG (Directed Acyclic Graph) execution structures. Decomposes tasks into nodes with dependencies and identifies candidate parallelization opportunities. Activate on 'build dag', 'create workflow graph', 'decompose task', 'execution graph', 'task graph'. NOT for simple linear tasks or when an existing DAG structure is provided.

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The intelligence layer of Jury-rig. Decomposes natural language tasks into proposed Hierarchical Task DAGs (HTDAGs), matches subtasks to skills, proposes wave and revision contracts, and expands nodes only when evidence supports a revised graph. Use for 'orchestrate', 'execute DAG', 'parallel agents', 'decompose task', 'coordinate skills'. NOT for single-skill tasks or simple linear workflows.

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Discipline an AI agent needs to work an issue/task tracker (Jira, Linear, GitHub Issues) as the shared source of truth: pull the right next item instead of inventing work, search before creating to avoid duplicates, write actionable items with checkable acceptance criteria, keep status transitions honest, and link work to items via branches/PRs/commits so progress is legible. Use when an agent picks up tracker work, files a new issue, updates status, or closes an item. NOT for authoring the PR itself (use agent-pr-authoring), roadmap-level planning and prioritization (use legible-roadmap-with-sidequests), or the mechanics of multiple agents coordinating on the same codebase (use multi-agent-coordination).

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Construct a finite oriented simplicial or cellular cochain model and compute its stated linear invariants when coefficient spaces, maps, metrics, and observations are explicit. Use for scoped Hodge, rank, or residual calculations; not for attributing agent intent or authorizing effects. NOT for attributing intent, identifying a liar, or authorizing external effects.

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Create and manage teams of specialized AI agents that work together on tasks. Use when setting up multi-agent workflows, agent squads for content/marketing/research pipelines, configuring heartbeat-based agent coordination, or managing agent personalities via SOUL.md files. Enables orchestration of multiple OpenClaw sessions as a coordinated team with shared task systems (Linear, Trello, etc.).

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Orchestrate autonomous AI development pipelines through your Kanban board (Asana, GitHub Projects, Linear). Manages multi-worker Claude Code dispatch, deterministic quality gates, adversarial review, per-task cost tracking, and crash-proof pipeline execution.

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54 real design systems (Stripe, Linear, Vercel) as HTML/CSS.

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Creates modern CSS gradients using Tailwind CSS including linear, radial, conic, mesh gradients, animated gradients, glassmorphism, and gradient text effects. Use when users request "gradient background", "tailwind gradient", "modern gradient", "mesh gradient", or "animated gradient".

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Use at the START of any bug bounty hunting session, when switching targets, or when feeling lost about what to do next. Master orchestrator that combines the 5-phase non-linear hunting workflow with the critical thinking framework (developer psychology, anomaly detection, What-If experiments). Routes to all other skills based on current hunting phase. Also use when asking 'what should I do next' or 'where am I in the process.'

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