“experiment”的搜索结果

Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical models. Covers signed-network choice, soft-threshold selection, module preservation, and the marginal-vs-partial-correlation distinction. Use when finding co-expression modules, identifying hub genes, relating gene networks to clinical or experimental traits, or building single-cell co-expression networks. For directed TF-target inference see scenic-regulons and grn-inference; for condition rewiring see differential-networks.

中文简介正在准备中。当前显示原文说明。

Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

中文简介正在准备中。当前显示原文说明。

Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.

中文简介正在准备中。当前显示原文说明。

Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

中文简介正在准备中。当前显示原文说明。

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.

中文简介正在准备中。当前显示原文说明。

Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.

中文简介正在准备中。当前显示原文说明。

Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

中文简介正在准备中。当前显示原文说明。

Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3 with constraints), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows.

中文简介正在准备中。当前显示原文说明。

Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

中文简介正在准备中。当前显示原文说明。

Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract, SES), k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

中文简介正在准备中。当前显示原文说明。

Use when introducing a feature flag system, choosing between release flags / experiment flags / operational flags / kill switches / permission flags, designing percentage rollouts, building kill-switch + circuit-breaker patterns, structuring evaluation contexts (user IDs, plan tier, region), or building flag-cleanup discipline. Triggers: LaunchDarkly / GrowthBook / Unleash / Flagsmith / OpenFeature, percentage ramp, sticky bucketing, kill switch wired to alerting, "we still have flags from 2 years ago", flag debt, OpenFeature provider, evaluation context, default value on provider failure. NOT for A/B test statistical analysis (separate skill), traffic-split routing at the edge, build-time bundler defines, or environment-based config.

中文简介正在准备中。当前显示原文说明。

Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.

中文简介正在准备中。当前显示原文说明。

Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.

中文简介正在准备中。当前显示原文说明。

The original v1 taste-skill, preserved for projects depending on its exact behavior. The current default is `design-taste-frontend` (v2 experimental), which is a substantial rewrite. Use this v1 install name only if you need exact backward compatibility.

中文简介正在准备中。当前显示原文说明。

Expert in statistical analysis for blind A/B and ABX audio testing. Validates randomization, calculates statistical significance, and ensures proper experimental design. Use when implementing A/B test features or analyzing test results.

中文简介正在准备中。当前显示原文说明。

Use when designing experiments for subject lines, offers, cadences, or journeys.

中文简介正在准备中。当前显示原文说明。

Design and analyze A/B tests, calculate statistical significance, and determine sample sizes for conversion optimization and experiment validation

中文简介正在准备中。当前显示原文说明。

Azure Weights & Biases SDK for .NET. ML experiment tracking and model management via Azure Marketplace. Use for creating W&B instances, managing SSO, marketplace integration, and ML observability.

中文简介正在准备中。当前显示原文说明。

Start a new OpenSpec change using the experimental artifact workflow. Use when the user wants to create a new feature, fix, or modification with a structured step-by-step approach.

中文简介正在准备中。当前显示原文说明。

Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.

中文简介正在准备中。当前显示原文说明。

Debug LLM applications using the Phoenix CLI. Fetch traces, analyze errors, review experiments, inspect datasets, and query the GraphQL API. Use when debugging AI/LLM applications, analyzing trace data, working with Phoenix observability, or investigating LLM performance issues.

中文简介正在准备中。当前显示原文说明。

Launch new products from idea to first customers. Use when launching products, finding early adopters, building launch week playbooks, diagnosing why adoption stalls, or learning that press coverage does not equal growth. Includes the three-layer diagnosis, the 2-week experiment cycle, and the launch that got 50K impressions and 12 signups.

中文简介正在准备中。当前显示原文说明。

Write ML papers for NeurIPS/ICML/ICLR: design→submit.

中文简介正在准备中。当前显示原文说明。

Build features guided by data insights, A/B testing, and continuous measurement using specialized agents for analysis, implementation, and experimentation.

中文简介正在准备中。当前显示原文说明。