「sic」の検索結果

Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier handling, VST/rlog transforms, and design formulas including paired, batch, and interaction terms. Use when running bulk DE, choosing DESeq2 over edgeR or limma-voom, building a paired or interaction design, applying LFC shrinkage for ranking or GSEA, choosing Wald vs LRT, troubleshooting padj=NA, picking VST vs rlog, importing salmon/kallisto via tximport, or analyzing prokaryotic RNA-seq.

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Assigns isolate identity at the right resolution for the question -- ANI / Mash species triage, 7-locus MLST historical comparability, cgMLST / wgMLST outbreak resolution (chewBBACA, BIGSdb, Ridom SeqSphere, EnteroBase HierCC), in-silico serotyping (SISTR, SeqSero2 for Salmonella; SerotypeFinder for E. coli; Kaptive K/O for Klebsiella; SeroBA for pneumococcus; spa + SCCmec for S. aureus), and lineage callers (TB-Profiler / Mykrobe Coll-Napier barcode for MTBC, Pangolin + Nextclade for SARS-CoV-2, PopPUNK GPSC for S. pneumoniae). Use when typing bacterial isolates for surveillance or outbreak investigation, choosing between cgMLST allele distance and core-SNP distance for cluster definition, harmonising calls across schemas / database versions (chewBBACA vs Ridom vs EnteroBase), assigning MTBC lineage with the Napier 2020 90-SNP barcode, calling Salmonella serovar via SISTR with monophasic Typhimurium awareness, running Pangolin UShER mode with explicit pangolin-data version pinning, or selecting a typing resolution to match the surveillance question.

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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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Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.

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Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, DIP). Use when building PPI networks, choosing between physical vs functional vs genetic interactions, signed/directed vs undirected, high-throughput vs curated, picking confidence thresholds, aggregating across resources, or navigating license constraints. Encodes the database decision matrix, STRING v12 channel semantics, OmniPath as meta-database, SIGNOR for signed signaling, and per-resource rate limits.

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Build publication-quality figures in R with ggplot2 using the grammar of graphics (data + aesthetics + geometries + scales + facets + themes) with CVD-safe palettes, cairo_pdf TrueType embedding, programmatic aes via tidy evaluation, and the theme_classic publication baseline. Use when producing static figures in R for papers, presentations, or reports.

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Extracts and assigns COSMIC v3.4 mutational signatures (84 SBS / 11 DBS / 18 ID / 24 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF, SigNet, or HRDetect. Use when characterizing DNA-damage etiology (BRCA1/2 HRD, MMR-D, POLE, APOBEC3A, UV, tobacco, aflatoxin, 5-FU/SBS17b, platinum, colibactin SBS88), routing PARP inhibitor decisions, or auditing de novo extraction vs refit choice for cohort size.

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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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Designs covalent inhibitors and warheads targeting cysteine (most common, 98% of covalent drugs), lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (TCI), KRAS G12C-style approaches, or rationalizing covalent SAR.

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View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.

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Use when an owner-operator (1099 or LLC/S-corp) asks how to lower their tax bill, what they can deduct, per diem treatment, depreciation choices (Section 179, bonus, MACRS), quarterly estimated payments, S-corp salary vs distributions, retirement plan options (SEP-IRA, Solo 401(k)), or recordkeeping requirements. Covers federal income tax + self-employment tax basics; not state-specific.

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Use this skill when the user asks about hazardous materials (hazmat) transportation under 49 CFR 171-180 — placarding requirements, segregation tables, hazmat employee training (49 CFR 172 Subpart H), Hazmat Safety Permit (HMSP), shipping papers, packaging groups, emergency response phone, security plans, hazmat endorsement on CDL, and bulk vs non-bulk distinctions. Cite specific 49 CFR section.

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Use this skill when the user asks how to interpret a DOT medical examiner's findings — what restrictions mean (corrective lenses, hearing aid, no insulin, etc.), what conditions trigger short-term vs 24-month certificates, vision/hearing thresholds, blood pressure categories, sleep apnea screening, when to seek an exemption program, and how to handle a downgrade or denial. Cite 49 CFR 391.41-49 and the FMCSA Medical Examiner Handbook.

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Use this skill when the user asks about DataQ — FMCSA's data review system at dataqs.fmcsa.dot.gov — for disputing inspection violations, crash records, or other entries that appear in a carrier's CSA / SMS score. Covers Request for Data Review (RDR) process, success rates, common dispute grounds, what evidence to attach, timeline expectations, and how successful disputes reduce BSI (BASIC Severity Indicator) scores. Cite 49 CFR 392.7 and the FMCSA DataQs User Guide.

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Use this skill to understand how FMCSA calculates the Crash Indicator BASIC. Covers what crashes count, severity weighting, time weighting, and the preventability program.

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Improve Coval trace quality after basic ingestion works. Use when traces are sparse, missing useful STT/LLM/TTS/tool spans, missing attributes needed for Coval built-in metrics, or when a customer wants maximum debugging and observability value from agent traces.

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RichDocument action toolkit for markdown and interactive content outside live chat. Use when adding an action or content source, wiring a remote action surface, putting actions on a MarkdownStream/BasicMarkdownContent preview, or touching features/rich-document/**, <RichDocument>, <RichDocumentActionSurface>, registerAction, ContentSourceAdapter, or enableContextMenu. NOT for the live chat message bar (use overlay-system).

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Use when the user asks to inspect Sentry issues or events, summarize recent production errors, or pull basic Sentry health data via the Sentry API; perform read-only queries with the bundled script and require `SENTRY_AUTH_TOKEN`.

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Three.js materials - PBR, basic, phong, shader materials, material properties. Use when styling meshes, working with textures, creating custom shaders, or optimizing material performance.

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Pushes interfaces past conventional limits with technically ambitious implementations — shaders, spring physics, scroll-driven reveals, 60fps animations. Use when the user wants to wow, impress, go all-out, or make something that feels extraordinary.

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PSR-1 and PSR-12 coding standards knowledge base for PHP 8.5 projects. Provides quick reference for basic coding standard and extended coding style with detection patterns, examples, and antipattern identification. Use for code style audits and compliance reviews.

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Search academic paper repositories (arXiv, Semantic Scholar) for scholarly articles in physics, mathematics, computer science, quantitative biology, AI/ML, and related fields

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3D web graphics with Three.js (WebGL/WebGPU). Capabilities: scenes, cameras, geometries, materials, lights, animations, model loading (GLTF/FBX), PBR materials, shadows, post-processing (bloom, SSAO, SSR), custom shaders, instancing, LOD, physics, VR/XR. Actions: create, build, animate, render 3D scenes/models. Keywords: Three.js, WebGL, WebGPU, 3D graphics, scene, camera, geometry, material, light, animation, GLTF, FBX, OrbitControls, PBR, shadow mapping, post-processing, bloom, SSAO, shader, instancing, LOD, WebXR, VR, AR, product configurator, data visualization, architectural walkthrough, interactive 3D, canvas. Use when: creating 3D visualizations, building WebGL/WebGPU apps, loading 3D models, adding animations, implementing VR/XR, creating interactive graphics, building product configurators.

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。

2D game development principles. Sprites, tilemaps, physics, camera.

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。