Results for “replicate”

Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way. Covers the genome-equivalent currency (~330 haploid copies/ng), the lambda = input_GE x VAF sampling ceiling (lambda>=3 for ~95% detection), the error-suppression ladder (raw NGS ~1e-3 -> single-strand UMI ~1e-4/1e-5 -> duplex <1e-7), the CLSI EP17 LoB/LoD/LoD95/LoQ framework, the per-locus-vs-panel-integrated LoD distinction that lets bespoke MRD reach ppm, contrived/SEQC2 reference standards, and honest LoD reporting conditioned on input mass + consensus depth + replicate detection rate. Use when stating or trusting a sensitivity claim, designing a dilution-series validation, deciding how many genome equivalents are needed at a target VAF, choosing a single-locus vs panel-integrated LoD, or auditing a "detects 0.1% VAF" claim.

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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.

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Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, deciding whether to repeat or rescue a screen, diagnosing low-confidence hits, choosing between MAGeCK / BAGEL2 / Chronos based on quality grade, picking a normalization strategy from QC signatures, or evaluating whether an in-vivo screen retained adequate library complexity.

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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.

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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

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Create premium hand-drawn architecture and process diagrams in the Lanshu animated GIF style, with editable .excalidraw files, static PNG previews, and genuinely animated GIFs with moving flow highlights. Use this skill whenever the user asks for 岚叔动态架构图, Excalidraw-like diagrams, DailyDoseOfDS-style black-background sketches, animated architecture/process GIFs, polished flowcharts, visual explanations of articles or system designs, or asks to replicate or improve a reference diagram with hand-drawn animated effects.

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Analyze images, video, speech, motion, products, and websites; route local vision, audio, depth, tracking, matting, identity, and restoration models; auto-edit, replicate, enhance, caption, voice, assemble, annotate, validate, and export editable Timeline Studio projects and videos. Use for reference-video remakes, filter and repeated-shot reconstruction, subject-aware reframing, clip splitting, source-time speed curves, Color Wheels grading, ramps and holds, person or product cutout, person or object outline, authorized face swap, shot and timing reconstruction, timeline markers, chapters, beat cues, review notes and ranges, supplied or web-sourced footage, AI video platform selection, cleanup, highlights, product promotion, website walkthroughs, image-to-video assisted edits, optical-flow editing, depth-assisted relighting, grayscale depth-video conversion, depth/2.5D/transition finishing, AI voiceover, subtitles, short-form production, .timeline automation, or editor evaluation.

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Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments – to facilitate global integrative studies. HiC-DC+ estimates significant interactions in a Hi-C or HiChIP experiment directly from the raw con

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Expert knowledge for Azure Web PubSub development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when building WebSocket/MQTT apps, Socket.IO chat, geo-replicated hubs, custom domains, or autoscale deployments, and other Azure Web PubSub related development tasks. Not for Azure SignalR Service (use azure-signalr-service), Azure Event Hubs (use azure-event-hubs), Azure Service Bus (use azure-service-bus).

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Write a publication-ready article in one of three angles - a trending long-form piece, a watched-repo thesis, or a project-through-a-lens essay. Optional Replicate hero image with --visual.

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Clone any website into a pixel-perfect single-file HTML prototype. Extracts design tokens, assets, CSS computed styles, interaction patterns, and content via Playwright. Outputs a self-contained HTML file with real data injection. Use when the user wants to clone, replicate, reverse-engineer, or create a pixel-perfect copy of any website or web app. Provide one or more target URLs as arguments.

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Reverse-engineer raw materials (Sparse idea, Dense idea, experimental log) from an existing AI research paper to build a benchmark case for evaluating paper-writing pipelines. Replicates the PaperWritingBench dataset construction procedure from arXiv:2604.05018 §3 / App. C. TRIGGER when the user asks to "build a benchmark case from this paper", "reverse-engineer raw materials", or "evaluate my pipeline against PaperWritingBench".

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Use when the next period content plan must be built from last period DATA — keep and replicate winners, cut losers, at most two new hypotheses, a 70/20/10 mix, a four-week overview, and an owner per slot. Trigger on 'next content plan', 'content plan for next month', 'plan from the audit', 'what should we post next quarter', 'scale what worked', 'plan content using the numbers'. Also use when a report just landed and the user asks what to do with it. Not for — auditing the past period first, see `39-content-audit-global`; turning the plan into a dated calendar, see `01-content-calendar-global`; the next period ADS plan, see `57-next-ads-plan-global`.

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AI image generation with OpenAI, Google, DashScope and Replicate APIs. Supports text-to-image, reference images, aspect ratios. Sequential by default; parallel generation available on request. Use when user asks to generate, create, or draw images.

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Reverse-engineer and clone a website in one shot — extracts assets, CSS, and content section-by-section and proactively dispatches parallel builder agents in worktrees as it goes. Use this whenever the user wants to clone, replicate, rebuild, reverse-engineer, or copy any website. Also triggers on phrases like "make a copy of this site", "rebuild this page", "pixel-perfect clone". Provide the target URL as an argument.

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Designs, sanity-checks and reads out product experiments (A/B tests, holdouts, pre/post, geo and incrementality tests) and produces an experiment brief plus a readout with a ship / hold / replicate call. Use when you ask 'should we A/B test this', 'how long should the test run', 'is this result real', 'sample size', 'stat sig', 'SRM', 'holdout', 'our win rate is low', or need to grade an existing test plan or readout. Draws on 191 insights from 71 Lenny's Podcast guests, led by Ronny Kohavi, Ramesh Johari and Archie Abrams.

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End-to-end paper reproduction from arxiv URL through smoke runs to replication experiments. Handles missing or partial official code, missing training scripts, missing hyperparameters, and private datasets via similar-public-dataset substitution. Use when the user asks to reproduce, implement, replicate, or re-run a paper from scratch, or pastes an arxiv URL with reproduction intent.

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Cancer Research (AACR) figures: resolution (300-1200 DPI), formats (EPS/TIFF/AI), hierarchical panel labels (Ai, Aii, Bi), figure/table limits, legend requirements with replicate counts.

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Use when applying a published cohort study's methodology to a different database. Extracts the design from the source paper, maps variables to the target database with a harmonization table, generates the analysis code and reports every forced deviation.

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