「pair」の検索結果

Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

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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.

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Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when BLAST fails to find homologs that should exist, when working at metagenomic scale (DIAMOND, MMseqs2), or when structure beats sequence (Foldseek). Covers PSI-BLAST (iterative PSSM), jackhmmer (iterative HMM), HHblits/HHsearch (profile-profile), DIAMOND, MMseqs2, and Foldseek (3Di structural alphabet, van Kempen 2024).

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Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indicator species (indicspecies IndVal.g group-equalized), PERMANOVA paired MANDATORILY with PERMDISP (Anderson & Walsh 2013; dispersion confounds centroid tests), Joint Species Distribution Models (HMSC, sjSDM, gjam) with explicit rejection of "residual covariance equals biotic interaction", phylogenetic community ecology (SES_MPD/MNTD), trait-environment via RLQ + fourth-corner with corrected modeltype=6 (Dray 2014), bipartite network metrics (NODF, modularity) with curveball null (Strona 2014), and Mantel-test replacements (dbRDA, GDM) for spatial data. Use when testing how environmental gradients structure communities, identifying habitat indicator taxa, partitioning variance among predictors, deciding whether PERMANOVA significance is location vs dispersion, picking among HMSC/sjSDM/gjam, or replacing Mantel tests for landscape data.

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Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with correct test selection (parametric vs non-parametric vs paired), multiple-testing adjustment, and rendering of negative results. Use when a boxplot/violin/raincloud needs in-figure statistical comparisons between groups.

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Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.

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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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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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Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

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Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and reaction templates, with explicit handling of atom mapping, RDChiral template extraction, product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.

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Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), mSINGS, and MANTIS for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen). Use when analyzing categorical outcomes, paired binary endpoints, or testing treatment-outcome independence in confirmatory or exploratory clinical trials.

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Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

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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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Use when work crosses into Apple's system surfaces rather than your own UI or data — Siri and Shortcuts, widgets, Live Activities, in-app purchase, localization, privacy prompts, alarms, timers, calendar, reminders, contacts, SharePlay, VoIP and CallKit, accessory pairing, weather, Spotlight indexing, background tasks, Background Assets, push, or push on networks with no internet.

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Apply Swift API Design Guidelines to name, label, and document Swift APIs. Covers argument label rules (prepositional phrase rule, grammatical phrase rule, first-label omission), mutating/nonmutating pair naming (-ed/-ing participle pattern, form- prefix, sort/sorted, formUnion/union), side-effect naming (noun for pure, verb for mutating), documentation comment structure (summary by declaration kind, O(1) complexity rule), clarity at call site, role-based naming, protocol naming (-able/-ible/-ing), default arguments over method families, casing conventions, and terminology. Use when designing new Swift APIs, reviewing naming and argument labels, writing documentation comments, or refactoring for call site clarity.

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Implement AlarmKit alarms and countdown timers for iOS and iPadOS with Lock Screen, Dynamic Island, StandBy, and paired Apple Watch system UI. Covers AlarmManager scheduling, AlarmAttributes and AlarmPresentation, system Stop and AlarmButton secondary actions, authorization, state observation, countdown widget-extension handoff, and Live Activity integration. Use when building wake-up alarms, countdown timers, or alarm-style alerts that need Apple's system alarm experience.

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Set up, repair, or migrate to Cloudflare Turnstile bot verification in an existing frontend and backend, including server-side Siteverify.

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Generate GNSS baseband waveforms (GPS, Galileo, NavIC) with physically realistic or user-specified channel impairments using the Satellite Communications Toolbox. Use when generating GPS L1 C/A, L1C, L2C, L5, Galileo E1, E1C, E5a, E5b, E5, or NavIC L5, S, L1 signals. Covers gpsWaveformGenerator, galileoWaveformGenerator, satelliteScenario, Doppler/delay from orbital dynamics or custom values, navigation data encoding with ephemeris, and RINEX integration. Triggers on: GPS waveform, Galileo waveform, NavIC waveform, GNSS signal, satellite scenario, GNSS simulation, receiver test signal, baseband GNSS, L-band satellite signal, navigation signal generation.

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Set up worker environment and per-worker state for parallel pools. Use when code needs paths, environment variables, database connections, loaded libraries, or expensive objects available on workers before parfor/parfeval runs. Teaches parallel.pool.Constant, parfevalOnAll, and parpool name-value pairs. Also use when refactoring existing code that uses spmd for side-effect setup (an anti-pattern). Triggers: worker setup, pool constant, per-worker state, non-serializable, loadlibrary on workers, database connection parfor, addpath workers, spmd before parfor, worker environment, reduce parfor overhead, parfor setup, resource creation in parallel loop, cannot serialize error, undefined function or variable on workers error, load data per worker, reduce data transfer, parallelize setup, improve parallel code.

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AWS EC2 virtual machine management — instances, security groups, key pairs, AMIs, EBS volumes, Auto Scaling Groups, Spot Instances, Session Manager, placement groups, and instance lifecycle automation. Trigger on ANY of these, even when EC2 isn't named explicitly: - Launching or provisioning: "spin up a server", "create a VM", "new instance", "run-instances", mention of instance types (t3, m5, c5, r6, g5, p4d, t4g, c7g, etc.) - SSH / connectivity problems: "connection refused", "connection timed out", "permission denied publickey", "can't connect to my instance", "SSH not working" - Instance management: resize, stop, start, terminate, reboot, change instance type - Cost optimization: stop dev instances overnight, save money on EC2, spot vs on-demand, reserved instances - Auto Scaling: ASG, launch template, mixed instances policy, scale to zero, scheduled scaling - Spot Instances: spot fleet, spot interruption, capacity-optimized, price-capacity-optimized - AMIs and backups: create image, custom AMI, EBS snapshot, DLM lifecycle policy, copy AMI - Monitoring: EC2 CPU utilization, CloudWatch metrics for instance, instance status checks, console output - Access methods: Session Manager, EC2 Instance Connect, bastion host, port forwarding - Security: IMDSv2, instance metadata, IAM role on instance, security group rules - User data and bootstrap scripts, cloud-init

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Manage EC2 instances, AMIs, and auto-scaling groups. Configure security groups, key pairs, and instance types. Use when deploying compute resources on AWS.

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