'compare' 검색 결과

Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.

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Compare cell-type composition and spatial features across conditions in IMC/MIBI cohorts with the patient as the experimental unit, covering pseudoreplication, per-patient aggregation, mixed models, compositional (Dirichlet/scCODA) differential abundance, diffcyt, per-image-to-patient spatial differential testing (SpaceANOVA), batch covariates, and FDR. Use when testing whether a cell type or spatial niche differs between groups, avoiding cell-level pseudoreplication, choosing a differential-abundance method, or correctly powering an IMC cohort comparison.

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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scaling; MetaPlotR; deepTools `computeMatrix scale-regions`), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (bigWig of log2 IP/input via deepTools `bamCompare`; ggcoverage; pyGenomeTracks; Gviz; IGV / UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), 5'UTR / CDS / 3'UTR stacked-bar feature-distribution summaries, and volcano / MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012 *Nature* 485:201; Meyer 2012 *Cell* 149:1635 — concurrent founding papers from different labs both showed this independently). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features for figure 1, generating DRACH motif logos as sanity checks on the peak set, rendering volcano plots of differential m6A, or reproducing the Dominissini 2012 / Meyer 2012 stop-codon enrichment plot.

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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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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautomer canonicalization, stereochemistry standardization, mixture handling, and isotope normalization. Explicitly compares ChEMBL pipeline, canSARchem, and PubChem standardization choices. Use when preparing libraries for QSAR training, joining datasets across sources, deduplicating compound collections, or building canonical compound registries.

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This skill should be used when the user asks to "implement LLM-as-judge", "compare model outputs", "create evaluation rubrics", "mitigate evaluation bias", or mentions direct scoring, pairwise comparison, position bias, evaluation pipelines, or automated quality assessment.

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Diff a live page's accessibility violations against a baseline — by default compares uncommitted changes (stash-based), or pass --branch [<name>] to diff against a branch. Reports only new violations introduced, violations fixed, and pre-existing count. Use `scan` for a full audit with no diffing.

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Extract study sites, observational variables, coordinates, climate-forcing sources, and cited data sources from ecosystem-modeling papers, PDFs, supplements, or article text, then plan or create EcoSIM simulation workflows and run folders for those sites. Use when Codex is asked to read a paper for EcoSIM feasibility, including requests phrased as "read paper for ecosim feasibility"; read a paper for sites/data availability; reproduce a published site simulation in EcoSIM; compare EcoSIM outputs to paper observations; or convert paper-derived AmeriFlux, FLUXNET, US NLDAS-domain, non-US ERA5, crop, peatland, forest, grassland, wetland, or unmanaged field-site information into EcoSIM inputs and runnable cases.

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Convert AmeriFlux ERA5 half-hourly meteorological CSV files into EcoSIM hourly climate forcing NetCDF files, compare generated forcing against overlapping measured tower meteorology when a FULLSET file is available, and report large biases or errors. Use when preparing or validating EcoSIM climate inputs for AmeriFlux sites, checking ERA5 against in situ records, diagnosing forcing discrepancies, or writing climate-quality reports. For non-AmeriFlux paper sites that need a fresh Copernicus CDS ERA5 point download by longitude/latitude, use era5-cds-point-download first.

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Edit EcoSIM PFT-parameter NetCDF files such as ecosim_pftpar_20260303.nc with the ParEditor class from applications/notebooks/scripts/ParamEditor.py. Use when asked to modify, scale, copy, compare, or delete PFT parameter records for a plant functional type (six-character pfts code such as gr3s43 or ndlf34), update microbe parameter NetCDF values, or maintain the JSONL change log that records past parameter changes. Never modify plant_trait.*.desc files; they are read-only references.

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Use this skill instead of WebSearch for ANY question requiring web research. Trigger on queries like "what is X", "explain X", "compare X and Y", "research X", or before content generation tasks. Provides systematic multi-angle research methodology instead of single superficial searches. Use this proactively when the user's question needs online information.

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Review or refactor an existing SKILL.md and its bundled resources — a smaller always-loaded core, conditional references, preserved behavior, lean/guided consumer profiles, and an A/B protocol to compare a candidate with the previous version. Use when a skill repeats itself, loads references on every run, triggers too broadly or misses legitimate requests, or needs its efficiency measured across models. Do NOT use for writing a new skill from scratch, refactoring application code, translating a skill verbatim, or performing the target skill's own task.

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When the user wants to create competitor comparison or alternative pages for SEO and sales enablement. Also use when the user mentions 'alternative page,' 'vs page,' 'competitor comparison,' 'comparison page,' '[Product] vs [Product],' '[Product] alternative,' 'competitive landing pages,' 'how do we compare to X,' 'battle card,' or 'competitor teardown.' Use this for any content that positions your product against competitors. Covers four formats: singular alternative, plural alternatives, you vs competitor, and competitor vs competitor. For sales-specific competitor docs, see sales-enablement.

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Live developer experience audit. Uses the browse tool to actually TEST the developer experience: navigates docs, tries the getting started flow, times TTHW, screenshots error messages, evaluates CLI help text. Produces a DX scorecard with evidence. Compares against /plan-devex-review scores if they exist (the boomerang: plan said 3 minutes, reality says 8). Use when asked to "test the DX", "DX audit", "developer experience test", or "try the onboarding". Proactively suggest after shipping a developer-facing feature. (gstack) Voice triggers (speech-to-text aliases): "dx audit", "test the developer experience", "try the onboarding", "developer experience test".

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Performance regression detection using the browse daemon. Establishes baselines for page load times, Core Web Vitals, and resource sizes. Compares before/after on every PR. Tracks performance trends over time. Use when: "performance", "benchmark", "page speed", "lighthouse", "web vitals", "bundle size", "load time". (gstack) Voice triggers (speech-to-text aliases): "speed test", "check performance".

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Post-deploy canary monitoring. Watches the live app for console errors, performance regressions, and page failures using the browse daemon. Takes periodic screenshots, compares against pre-deploy baselines, and alerts on anomalies. Use when: "monitor deploy", "canary", "post-deploy check", "watch production", "verify deploy". (gstack)

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Preview and verify imported content in local AEM Edge Delivery Services dev server. Validates rendering, compares with original page, and troubleshoots common issues.

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Comprehensive dimension analysis and reporting for CJA. Use this skill whenever the user wants to analyze one or more dimensions — including cardinality, distribution/skew, trends, anomalies, data quality errors, comparisons, and forecasting. Also trigger when someone asks "what are the top values for...", "dimension health", "explore this dimension", "dimension dashboard", "dimension statistics", "data quality check on a dimension", "dimension cardinality", "dimension trends", "dimension skew", "dimension anomalies", "compare dimensions", or any similar request to understand what's inside a CJA dimension. Produces an interactive HTML dashboard or a markdown report. Works with the CJA MCP server.

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Compare two versions of an AEM Edge Delivery Services page to identify what changed. Fetches preview vs live, or two different URLs, and produces a detailed content diff showing added, removed, and modified content, metadata, and blocks. Use when reviewing changes before publishing, auditing content modifications, or tracking content evolution.

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BROWSER REVIEW QA SKILL — Use the built-in browser/headless browser (puppeteer-core) to open a browser-runnable Cocos preview, switch preview targets, capture screenshots, and compare them with reference images. USE FOR: screen-driven QA only when the user has already prepared a Browser Review environment that can run in the browser (`http://localhost:7456`, LoadingScene/preview host/preview target wiring ready). DO NOT USE FOR: current Cocos Editor window screenshots, Editor Preview capture, compile errors, or pure log analysis. If the Browser Review environment is not ready, stop and remind the user to prepare it first.

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Agent context budget guard and artifact compression workflow. USE FOR: image-heavy QA, compare board review, screenshot batches, large keep/todo/task manifests, long notes handoff, and md/json diff summarization. Trigger this before reading or forwarding heavy artifacts when token growth is a risk.

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Score LLM and agent outputs using LLM-as-judge techniques — direct scoring against rubrics or pairwise comparison between two outputs. Includes built-in bias mitigation for position bias, length bias, and self-enhancement bias. Load when the user asks to score an output, judge a response, evaluate against a rubric, compare two outputs, do direct scoring, run pairwise comparison, or says "rate this", "which response is better", "score this against the rubric", "judge this output", "LLM as judge this". Sub-skill of eval-output orchestrator.

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