「inference」の検索結果

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

日本語の概要は準備中です。原文の説明を表示しています。

Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.

日本語の概要は準備中です。原文の説明を表示しています。

Estimate bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitivity battery. Cross-trait LDSC intercept absorbs sample overlap and is NOT a bias; HDL is biased under sample overlap above ~5%. High rg between exposure and outcome motivates CHP-aware MR sensitivity (CAUSE, LHC-MR).

日本語の概要は準備中です。原文の説明を表示しています。

Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

日本語の概要は準備中です。原文の説明を表示しています。

Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth.

日本語の概要は準備中です。原文の説明を表示しています。

Audits GitHub Actions workflows for security vulnerabilities in AI agent integrations including Claude Code Action, Gemini CLI, OpenAI Codex, and GitHub AI Inference. Detects attack vectors where attacker-controlled input reaches. AI agents running in CI/CD pipelines.

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Review a Go design spec before implementation begins - dispatch a subagent that checks a design doc for completeness, consistency, and idiomatic Go (simplicity, small consumer-defined interfaces, explicit wrapped errors, context propagation) plus Cobra/Viper conventions where applicable. Use when a user has a Go spec to review, asks "is this spec ready?", or is about to implement from a written design. Distilled from spf13/go-skills and adapted to this repo's conventions.

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Idiomatic Go - package and interface design, error wrapping, table-driven tests, generics, the modern standard library (slices/maps/cmp/errors.Join), current syntax, and logging discipline. Use when writing, reviewing, or refactoring any Go code, especially code drifting toward Java/Spring shapes (deep layer trees, generic repositories, heavy frameworks) - even if the user never says "idiomatic". Distilled from spf13/go-skills and adapted to this repo.

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Idiomatic Go concurrency - sync primitives, channel semantics, the select statement, and the standard channel patterns (cancellation/done-channel, fan-out/fan-in, pipeline, or-done, context, worker-pool). Use when writing or reviewing Go that spawns goroutines, shares state, or coordinates over channels, even if the user never says "concurrency" - e.g. data races, deadlocks, goroutine leaks, sync/context/select usage, or "make this parallel". Distilled from luk4z7/go-concurrency-guide.

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Instrument a shipped product's AI agents with tracing and observability so you can see what they did, why outputs happened, and what each run cost. Plain-language primer plus free-tier-first backend selection (Langfuse, Phoenix, LangSmith, Braintrust) and OpenTelemetry/OpenInference instrumentation. Load when the user asks to add observability, add tracing, instrument my agents, see what my agent is doing in production, set up Langfuse or Phoenix or LangSmith, debug why my agent gave a bad answer, or track LLM cost per request. Also fires when agent-system-architecture or setup-evaluation requires an observability plan for an agent-chain product. NOT for tracing the coding agent itself — that is run-trace. Precondition for runtime-learning-loop.

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Type-safe ORM for Cloudflare D1 using Drizzle. Use when building D1 schemas, writing type-safe queries, generating migrations with Drizzle Kit, defining relations, using db.batch, or hitting D1_ERROR, BEGIN TRANSACTION failures, foreign key constraints, env.DB undefined, or schema inference issues.

日本語の概要は準備中です。原文の説明を表示しています。

Audits GitHub Actions workflows for security vulnerabilities in AI agent integrations including Claude Code Action, Gemini CLI, OpenAI Codex, and GitHub AI Inference. Detects attack vectors where attacker-controlled input reaches. AI agents running in CI/CD pipelines.

日本語の概要は準備中です。原文の説明を表示しています。

Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

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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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Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion estimation from DESeq2/edgeR. Covers the biological-versus-technical replication distinction (technical replicates do not add degrees of freedom for biological inference), replicate-number-versus-sequencing-depth budgeting, scRNA-seq sample-versus-cell allocation under a pseudobulk model, and the critique that "n=3" is a publication convention rather than a power calculation. Use when budgeting a sequencing experiment, writing the sample-size justification in a grant, estimating replicates from pilot data, allocating a fixed budget between samples and depth, or planning scRNA-seq cohort size. For clinical-trial sample size see clinical-biostatistics/power-and-sample-size; for the power-given-n direction see experimental-design/power-analysis.

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Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.

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Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata. Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB / chronic HIV.

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Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and when to defect to de novo computation.

日本語の概要は準備中です。原文の説明を表示しています。

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

日本語の概要は準備中です。原文の説明を表示しています。

Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

日本語の概要は準備中です。原文の説明を表示しています。

Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.

日本語の概要は準備中です。原文の説明を表示しています。

Estimate bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitivity battery. Cross-trait LDSC intercept absorbs sample overlap and is NOT a bias; HDL is biased under sample overlap above ~5%. High rg between exposure and outcome motivates CHP-aware MR sensitivity (CAUSE, LHC-MR).

日本語の概要は準備中です。原文の説明を表示しています。

Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth.

日本語の概要は準備中です。原文の説明を表示しています。

Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

日本語の概要は準備中です。原文の説明を表示しています。