「profile」の検索結果

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 Salmonella, SerotypeFinder E. coli, Kaptive Klebsiella, SeroBA pneumococcus, spa+SCCmec S. aureus), and lineage callers (TB-Profiler/Mykrobe 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, assigning MTBC lineage with the Napier 90-SNP barcode, calling Salmonella serovar via SISTR with monophasic Typhimurium awareness, running Pangolin UShER mode with 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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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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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), TRIBE/HyperTRIBE (ADAR-RBP, A-to-I editing), DART-seq (APOBEC1-YTH for m6A), or Bullseye/SAILOR edit-site detection pipelines. Use when antibody is unavailable or specificity is doubtful, when single-cell RBP profiling is needed (scSTAMP), or when in vivo RBP profiling without UV is preferred.

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Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood, Bender NNT) and reports marginal vs conditional estimands per FDA 2023 covariate adjustment guidance. Use when reporting treatment effects in confirmatory trials, comparing effect sizes across studies, or constructing forest plots.

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Extracts and assigns COSMIC v3.4 mutational signatures (86 SBS / 11 DBS / 18 ID / 21 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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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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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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Infers genetic super-population ancestry from a 23andMe/AncestryDNA file and computes ancestry-stratified odds ratios with an exploratory Ancestry Elevation Score (AES) showing where ancestry-specific GWAS effect sizes diverge from European reference estimates.

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Evaluates cardiovascular risk factors in persons receiving hormone therapy by obtaining fasting lipid profiles and diabetes screening. Triggered when a patient is on gender-affirming hormone therapy and due for routine cardiovascular risk assessment.

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Guides comorbidity-stratified selection of initial and further glucose-lowering medicines for adults with type 2 diabetes using the NICE NG28 (2026) framework, covering six clinical profiles: no relevant comorbidity, heart failure, atherosclerotic cardiovascular disease, early onset, obesity, chronic kidney disease, and frailty.

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Write technical documentation that matches the measured profile of professionally-written docs. Carries the craft rules derived from 114k words of pre-2022 documentation (SQLite, PostgreSQL, Python, Django, Rust, Go, Pro Git, nginx), the per-Diátaxis-type numeric targets, and the copywriting register for page leads. Use when drafting or rewriting any documentation prose, or when a page is factually right but reads as machine-written.

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Standard operating procedure for producing a documentation page end to end — gather source material, classify, draft against the measured corpus profile, then run the reader-level and humanizer passes and both gates. Use for any page on a documentation surface, or when rewriting a page that reads as machine-written. Orchestrates technical-writing, reader-level and humanizer in a fixed order.

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Automate SEO research with Ahrefs -- analyze backlink profiles, research keywords, track domain metrics history, audit organic rankings, and perform batch URL analysis through the Composio Ahrefs integration.

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Use when Amazon Ads optimization analysis, recommendations, approval packets, demos, recordings, or public artifacts must preserve exact source KPIs while masking account/profile/project names, products, ASINs, SKUs, campaigns, ad groups, keywords, search terms, targets, placements, filenames, URLs, and source-derived identifiers. Produces masked approval packets only; it must not directly mutate Amazon Ads.

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Use for read-first Amazon Sponsored Products optimization, product-aware growth, preflight readiness, and post-change monitoring reviews that can run standalone from static exports or use Rocketcart MCP as an optional Amazon Ads plus product-intelligence layer. Guides Codex to inspect Rocketcart profiles, live SP campaigns, product ads/ASIN context, category rank/BSR movement, competitor signals, product readiness, budget and targeting drift, snapshots/changelogs, and proposed approval-gated action rows without executing writes by default.

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Audit social media accounts (TikTok, IG, etc.): scrape profiles, calculate engagement metrics, diagnose performance drops, interpret analytics screenshots.

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Decomposition playbook + specialist-roster conventions + anti-temptation rules for an orchestrator profile routing work through Kanban. The "don't do the work yourself" rule and the basic lifecycle are auto-injected into every kanban worker's system prompt; this skill is the deeper playbook when you're specifically playing the orchestrator role.

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Tests in real browsers. Use when building or debugging anything that runs in a browser. Use when you need to inspect the DOM, capture console errors, analyze network requests, profile performance, or verify visual output with real runtime data via Chrome DevTools MCP.

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Create a fresh NeatContext context from a user-defined behavioral profile and an existing local knowledge folder. Use only when the user explicitly invokes this skill or asks to create a new context rather than save the current conversation.

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Create a fresh NeatContext context from a user-defined behavioral profile and an existing local knowledge folder. Use only when the user explicitly invokes this skill or asks to create a new context rather than save the current conversation.

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Create a fresh NeatContext context from a user-defined behavioral profile and an existing local knowledge folder. Use only when the user explicitly asks to create a new context, or runs /neatcontext-create — not to save the current conversation.

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Check proposed stack, data flows, cloud choices, and delivery controls against declared enterprise policies, compliance frameworks, and security controls. Trigger at R2/R3 risk classification, before locking architecture decisions, or when the operating profile names a governance pointer.

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