'linear' 검색 결과

Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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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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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 calibration (BF >6 ≈ 90% posterior per Hart 2017; ~5% FDR by BAGEL convention). 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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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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Price financial instruments in MATLAB using the Financial Instruments Toolbox. Route to the appropriate numerical method reference based on the user's request: Monte Carlo simulation (AssetMonteCarlo, IRMonteCarlo, RoughVolMonteCarlo), FFT / Numerical Integration (Vanilla European options), or Interest-Rate Trees (option-embedded bonds with IRTree). Use when the user asks to price financial instruments or compute Greeks using any of these methods. Use one of the following models depending on the pricing method and instrument: Black-Scholes, Bachelier, Heston, Bates, Merton, Hull-White, Black-Karasinski, Black-Derman-Toy, Cox-Ingersoll-Ross, Linear Gaussian 2 Factor (G2PP), Brace-Gatarek-Musiela (BGM), SABR-BGM, RoughBergomi, RoughHeston.

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Use when grooming hair or fur in Maya with XGen (Interactive Groom splines or legacy descriptions): scalp hair, eyebrows, eyelashes, fur, guides, clumps, noise, parting, density maps, a fill layer, aiStandardHair shading, noisy or flickering hair renders, hair that must move (Linear Wire, nHair, Alembic caches), or a groom for Unreal (groom Alembic, cards). Also when XGen hair looks CG, clumps look uniform, the scalp shows through, or an XGen script fails.

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LP, MILP, and QP (beta) with cuOpt — Python, C, and CLI. Use when the user is solving LP, MILP, or QP with any cuOpt interface.

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LP, MILP, QP — concepts, problem-text parsing, and formulation patterns (parameters, constraints, decisions, objective). Concepts only; no API.

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Write complete, ready-to-pull work items for an issue tracker: bugs, tasks, stories, spikes, and epics, each with the fields, attachments, and done test its type requires. Use this skill whenever the user wants to write a ticket, create a Jira issue, Linear issue, or GitHub issue, file a bug report, write a user story or acceptance criteria, scope a spike, open an epic, or break work into tasks. Triggers on write a ticket, create an issue, file a bug, bug report, user story, spike, epic, task breakdown, turn this into tickets, break this down, acceptance criteria, definition of ready, ready for dev, backlog item, capitalization stage. Also triggers when the user pastes a PRD, a spec, or a bug description and asks what to do with it, even if they never say the word ticket.

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Generate a phased delivery orchestration plan for creative-direction-driven work: which skills run when, what locks at which gate, how handoffs occur, and how the cadence implements in the team's tools (Jira, Linear, Notion, Figma, GitHub) with AI agents via MCP and CLI. A temporal map of phases, lock points, handoff specs, gate definitions, and QA verification gates. Distinct from `creative-brief` (static project brief) and `creative-direction` (aesthetic direction). Triggers on integration orchestrator, delivery cadence, project orchestration, when does the brief lock, how to phase creative direction, design-development handoff, QA gate, agent-driven QA, and when a creative-direction project is starting, mid-flight with broken cadence, or integrating AI agents into PM workflow. Does NOT fire for project scoping (use `creative-brief`), aesthetic direction (use `creative-direction`), or general project management without a creative-direction throughline.

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Apply pre-composed aesthetic archetype defaults to jumpstart brand design work covering color, typography, layout, voice, and imagery direction. Use this skill whenever the user wants a starting point for brand visual and verbal direction, references a brand they want to design near (for example 'something like Stripe' or 'editorial like Linear'), needs to converge faster from many directions to one, or wants known-good defaults for a specific industry vertical. Triggers on archetype, design archetype, brand archetype, near to (brand), in the style of, similar aesthetic, design starting point, brand template, vertical-typical, industry-typical. Also triggers when the user has a brief and wants to map it to a known aesthetic family rather than design from first principles.

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Notion expert for product management workflows. Use for database design for PRDs/OKRs/Roadmaps/Decisions, property and view design, page architecture, Notion REST API, and sync with Jira, Linear, and GitHub.

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A switch whose knob springs across on toggle — a tactile, satisfying on/off state change. Use for settings/form switches. Honors prefers-reduced-motion (quick linear slide). Trigger on user intent only; keep the spring subtle — never to convey loading/progress.

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When you want to manage projects across your businesses using a kanban + Eisenhower methodology. One kanban per business (whatever portfolio of businesses, projects, or initiatives you run). Tool-agnostic — connects via API/MCP to whatever PM tool each business uses (Notion, GitHub Projects, Plane, Linear, Obsidian file-based, or manual mode). Async-first output. Six modes — setup (scaffold a new board for a business), triage (Eisenhower-sort the backlog), next (pick the next thing to work on, single board or across all), status (paste-ready async snapshot), unblock (diagnose Review/Blocked column), weekly (Friday pulse + week planning). Triggers on "/pm," "/pm setup," "/pm triage," "/pm next," "/pm status," "/pm unblock," "/pm weekly," "what should I work on next," "kanban status," "Eisenhower this," "triage my backlog," "what's blocked."

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Swift 6.2 InlineArray and Span types for zero-overhead memory access, fixed-size collections, and safe pointer alternatives. Use when optimizing performance-critical code paths.

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Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers spot and large technical artifacts. Scales linearly with the number of spots and is designed to be used with 'SpatialExperiment' objects.

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Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more

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Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.

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Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression

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Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA o

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Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix. Implements

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Build crafted, highly detailed, interactive isometric SVG figures that explain a technical idea as a real physical object (a test rig, a dial gauge, a cabinet of drawers, a plotter, a lock), with many small precise solid parts, four-tone shading, correct painter's order, a framed card with title, hint and live readout, and calm eased motion. Use this whenever someone wants an isometric illustration, an explanatory diagram or figure for docs, a blog post, a landing page or an article, a "Linear-style" or "premium" technical drawing, an interactive explainer, or an SVG that shows how a system, algorithm or component works, even if they never say "isometric". Works framework-free (TypeScript/JS that writes SVG and HTML) and in React/Next.js, and can add realistic WebGL shaders (fire, exhaust, water, caustics, lamp light) that live inside the drawing in the same isometric perspective.

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Token unlock and vesting tracker - quantify supply pressure via absorption ratio, classify cliff vs linear, and deliver one-line market reads

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Summarize and review what changed while you were away. Use after a weekend, vacation, or flight to check missed PRs, git commits, Linear tickets, and meetings — one prioritized brief, not a firehose.

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