「bi」の検索結果

Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, biomaRt, mygene, pyensembl, and Ensembl REST. Encodes Ensembl version stripping with GENCODE _PAR_Y preservation, the Ziemann 2016 Excel autocorrect debacle and Bruford 2020 HGNC renames (SEPT*->SEPTIN*, MARCH*->MARCHF*, MARC*->MTARC*, DEC1->DELEC1), OCT4/POU5F1 alias resolution, biomaRt archive endpoints for release pinning, the `filters` (plural) gotcha, MANE Select for clinical reporting, cross-species orthology via Ensembl Compara / OMA / OrthoDB, and tx2gene construction for tximport. Use when converting gene IDs across systems, handling renamed symbols, building tx2gene, pinning to a specific Ensembl release for reproducibility, or mapping cross-species orthologs.

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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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Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-analysis).

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and translates calls into WHO GLASS reporting categories. Use when screening clinical or surveillance isolates for AMR, distinguishing acquired vs intrinsic vs point-mutation resistance, calling rpoB / katG / pncA / gyrA / mgrB mutations, reconciling AMRFinderPlus vs RGI vs ResFinder disagreement, contextualising carbapenemases or mcr alleles on plasmids, predicting susceptibility from genotype against the WHO Mtb 2nd-edition catalogue, or building a hAMRonized multi-lab AMR surveillance pipeline.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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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.

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Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

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Estimates 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).

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Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS taxonomy.

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Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.

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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

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Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).

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Selects spironolactone as first-line mineralocorticoid receptor antagonist for bilateral primary aldosteronism, with eplerenone as an alternative when spironolactone–related adverse effects are problematic. Trigger phrases include 'confirmed bilateral PA on AVS', 'idiopathic adrenal hyperplasia', 'bilateral adrenal hyperplasia', 'glucocorticoid-remediable aldosteronism', and 'initiating medical therapy for bilateral adrenal disease'.

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Extract a DDD-style ubiquitous language glossary from the current conversation, flagging ambiguities and proposing canonical terms. Saves to UBIQUITOUS_LANGUAGE.md. Use when user wants to define domain terms, build a glossary, harden terminology, create a ubiquitous language, or mentions "domain model" or "DDD".

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Expert-level biophysics covering single molecule techniques, membrane biophysics, protein mechanics, motor proteins, ion channels, and biological imaging methods.

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Expert-level orbital mechanics covering Keplerian orbits, orbital maneuvers, Hohmann transfers, rendezvous, interplanetary trajectories, and perturbations.

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Expert-level biomechanics covering musculoskeletal mechanics, gait analysis, joint biomechanics, soft tissue mechanics, bone mechanics, and sports biomechanics.

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Evaluate UI/flows from cognitive load, error prevention, and accessibility perspectives. Apply when reviewing UX, discussing user confusion, high drop-off, or form usability issues.

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医学证据等级排序与编排层 skill - evidence grading orchestrator. 当用户请求"证据等级 / GRADE / 证据排序 / 医学证据评估 / 系统评价排序 / 临床证据排序 / 证据金字塔 / 给 PMID 打分 / Practice Guideline 优先 / Cochrane 优先 / 反向证据交叉验证 / evidence grading / quality of evidence / evidence pyramid / GRADE assessment / Cochrane review ranking / clinical evidence ranking"时,**调用本 skill 进行医学证据自动分级,自动选择最佳信息源**。本 skill 是编排层(L2)·不直接打 NCBI/Europe PMC/ClinicalTrials API,而是编排 6 个底层原子 skill(pubmed-eutils / europepmc-search / clinical-trials-v2 / aact-bulk-trials / bioc-fulltext-fetch / pubtator-entity-search)的召回结果,按证据金字塔(指南 > Meta > RCT > Cohort > Case-Control > Case Report)做 GRADE A/B/C/D 自动评级,自动剔除 editorial/letter/comment。优先使用 BioMCP MCP server 做 fan-out(genomoncology/biomcp);无 BioMCP 时走自建 slow-path 兜底。跨平台无锁(Claude Code / Codex / Gemini CLI)。

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医学证据等级排序与编排层 skill。当用户请求"证据等级 / GRADE / 证据排序 / 医学证据评估 / evidence grading / quality of evidence / 系统评价排序 / 临床证据排序 / 证据金字塔"时触发。本 skill 不直接调用 NCBI/Europe PMC/ClinicalTrials API,而是编排 6 个底层原子 skill(pubmed-eutils / europepmc-search / clinical-trials-v2 / aact-bulk-trials / bioc-fulltext-fetch / pubtator-entity-search)的召回结果,按 ChatGPT 推荐的证据金字塔(指南 > Meta > RCT > Cohort > Case-Control > Case Report)做 GRADE 自动评级,自动剔除 editorial / letter / comment。优先使用 BioMCP MCP server 做 fan-out(genomoncology/biomcp),无 BioMCP 时走自建 slow-path 兜底。

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Builds a structured vulnerability scanning workflow using tools like Nessus, Qualys, and OpenVAS to discover, prioritize, and track remediation of security vulnerabilities across infrastructure. Use when SOC teams need to establish recurring vulnerability assessment processes, integrate scan results with SIEM alerting, and build remediation tracking dashboards.

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Parses Software Bill of Materials (SBOM) in CycloneDX and SPDX JSON formats to identify supply chain vulnerabilities by correlating components against the NVD CVE database via the NVD 2.0 API. Builds dependency graphs, calculates risk scores, identifies transitive vulnerability paths, and generates compliance reports. Activates for requests involving SBOM analysis, software composition analysis, supply chain security assessment, dependency vulnerability scanning, CycloneDX/SPDX parsing, or CVE correlation.

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