「bias」の検索結果

Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number R_e, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict/relaxed clocks; coalescent, Bayesian-Skyline, Skygrid, Birth-Death-Skyline, and sampled-ancestor priors; structured coalescent via MASCOT). Covers root-to-tip clock QC via TempEst, date-randomisation tests, recombination masking via Gubbins/ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction, multi-chain convergence diagnostics, and reconciling phylodynamic R_e with case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline models, diagnosing temporal-signal failure, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

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Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, trials, or instruments — meta-analysis, Mendelian randomization, subgroup HRs.

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Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CAI codon-optimized sequences. Use when scoring a gene's codon bias against a host, optimizing a CDS for heterologous expression, or studying synonymous codon selection.

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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.

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Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.

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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.

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Marc Andreessen-mode decision and productivity skill. A blunt, market-first operator that pressure-tests ideas, ventures, features, and career bets through Andreessen's actual frameworks — market dominates team and product; the only milestone that matters is product/market fit; bias to build over deliberate. Use when the user says 'andreessen', 'pmarca mode', 'should I build this', 'is there a market', 'are we at product/market fit', 'pmf check', 'pressure-test this idea', 'be brutal about this venture', 'market-first take', or wants a no-disclaimers, no-hedging, confidence-leveled verdict on whether something is worth pursuing. Also provides the 3x5-card + Anti-Todo personal productivity routine. Runs on a fixed anti-sycophancy operating prompt: leads with the strongest counterargument, never validates premises, uses explicit confidence levels, never apologizes for disagreeing. Not for polite brainstorming — this skill exists to tell you the market is dead when it is.

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Use for ethical thinking, or when a plan could harm or unfairly burden people: "should we do this?", "is this fair?", "privacy or bias risk", "who gets hurt?". Maps stakeholders, harms, power and consent. Skip for legal advice, neutral fact lookups and implementation-only work.

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W&B: log ML experiments, sweeps, model registry, dashboards.

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When running discovery interviews — question-bank build, bias audit, insight extraction. Triggers on 'audit my guide', 'extract insights from transcript', 'is my hypothesis falsifiable'.

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Estenda janelas de contexto de modelos transformer usando RoPE, YaRN, ALiBi e técnicas de interpolação de posição. Use ao processar documentos longos (32k-128k+ tokens), estender modelos pré-treinados além dos limites de contexto originais ou implementar codificações posicionais eficientes. Cobre embeddings rotativos, vieses de atenção, métodos de interpolação e estratégias de extrapolação para LLMs.

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Automatic quality check on significant outputs via isolated sub-agent. Spawns reflection-agent for objective evaluation without conversation context bias.

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Econometrics skill for machine learning methods in causal inference. Activates when the user asks about: "causal forest", "generalized random forest", "GRF", "double machine learning", "DML", "debiased machine learning", "LASSO for variable selection", "post-LASSO", "heterogeneous treatment effects", "CATE", "conditional average treatment effect", "BLP analysis", "CLAN analysis", "causal tree", "honest estimation", "因果森林", "双重机器学习", "异质性处理效应", "条件平均处理效应", "LASSO变量选择", "机器学习因果推断", "去偏机器学习"

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Knowledge base from the NIST/SEMATECH e-Handbook of Statistical Methods (NIST HB 151) — the practical statistics reference for engineering, metrology, and quality. Use for: exploratory data analysis and the four univariate assumptions (4-plot); measurement process characterization including bias/precision, calibration designs, gauge R&R, and ISO/GUM uncertainty budgets; production process characterization (stability vs. capability); process modeling and regression (LS/WLS/NLS/LOESS); design of experiments (screening, fractional/factorial, response-surface, Taguchi); statistical process control (Shewhart/CUSUM/EWMA charts, capability indices, acceptance sampling); product/process comparisons (hypothesis tests and confidence intervals for 1/2/3+ groups, ANOVA, multiple comparisons); and reliability (lifetime & repair-rate models, accelerated testing, reliability growth). Scope limits: this is applied frequentist statistics for measurement and quality — it does NOT reproduce the per-distribution formula galleries, worked case studies, datasets, plot images, or Dataplot/R code of the original web Handbook (those are described, not copied); it is thin on modern machine learning, Bayesian methods beyond conjugate reliability priors, time-series/forecasting, and Bayesian experimental design.

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Knowledge base from NIST AI Risk Management Framework 1.0 (NIST AI 100-1). Use for AI risk management, trustworthiness characteristics, GOVERN/MAP/MEASURE/MANAGE functions, bias management, AI actor roles, TEVV, AI RMF profiles, and socio-technical risk framing. Does not cover sector-specific regulations, EU AI Act, ISO 42001 in depth, or the AI RMF Playbook tactical detail.

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Knowledge base from the NASA Schedule Management Handbook (2024 edition, Revision 2). Use for program/project schedule management of aerospace and large engineering efforts: the five sub-functions (Planning, Development, Assessment & Analysis, Maintenance & Control, Documentation & Communication); the Integrated Master Schedule (IMS) and the WBS/OBS/CBS breakdown structures; the Schedule Management Plan (SMP) and Basis of Estimate (BoE); Critical Path Method, logic, durations, float and margin; tiered schedule assessment (Requirements/Health/Basis checks, the Shock Test) and the Dimensions of Schedule Reliability; Schedule Risk Analysis (SRA), Integrated Cost-Schedule Risk Analysis (ICSRA), Monte Carlo, correlation, merge bias, and the Joint Confidence Level (JCL); baselining, replan vs. rebaseline, EVM schedule metrics (SPI, BEI, CEI, HMI, Earned Schedule, CPLI), and status/progress/forecast reporting. This is NASA's scheduling doctrine grounded in NPR 7120.5 and the GAO Schedule Assessment Guide. Thin on the underlying mechanics of CPM, statistics, and EVM (it points to companion handbooks); aerospace/space-flight-centric; anchored to the 2024 second edition.

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Daily wisdom review applying Charlie Munger's mental models to your work and thinking. Use when asked to review decisions, analyze thinking patterns, detect biases, apply mental models, do a "Munger review", or run the Munger Observer. Triggers on scheduled daily reviews or manual requests like "run munger observer", "review my thinking", "check for blind spots", or "apply mental models".

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When the user wants to apply psychological principles, mental models, or behavioral science to marketing. Also use when the user mentions 'psychology,' 'mental models,' 'cognitive bias,' 'persuasion,' 'behavioral science,' 'why people buy,' 'decision-making,' 'consumer behavior,' 'anchoring,' 'social proof,' 'scarcity,' 'loss aversion,' 'framing,' or 'nudge.' Use this whenever someone wants to understand or leverage how people think and make decisions in a marketing context. For applying psychology to specific pages, see cro; for pricing tactics, see pricing; for copy framing, see copywriting.

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