“init”的搜索结果

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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Infers person-to-person transmission from pathogen genomes using outbreaker2, TransPhylo, phybreak, BadTrIP, SCOTTI, BEASTLIER, 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; MRSA <=15; C. difficile <=2; Klebsiella <=21), models within-host diversity and transmission bottlenecks, integrates contact-tracing data, distinguishes generation from serial interval, and attributes source via Bayesian source attribution (islandR). 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 a 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 or chronic HIV.

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Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions), hyperparameter sensitivity, and the well-documented limits of 2D embeddings. Covers PCA biplot/scree/loadings, t-SNE PCA initialization (Kobak-Berens 2019), UMAP n_neighbors/min_dist trade-offs, and the Chari-Pachter 2023 critique. Use when visualizing high-dimensional data — bulk PCA, single-cell embeddings, multi-omics integration projections.

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CA-CTCF/CA-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.

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Recognize which awakening stage consciousness is navigating through. Use when diagnosing seeker development, identifying stage transitions, or recognizing readiness levels. Covers 7 stages from initial dissatisfaction through natural flow mastery.

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Set up a parallel agent team for COMPLEX tasks: creates worktree structure, an ownership map, and an initialized task queue. Use when a task is decomposed into parallel subtasks.

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Structured second-pass reasoning after a review or plan verdict: pre-mortem, inversion, red team, Socratic lens, etc. NOT for initial review (mk:review) or new plans (mk:plan-creator).

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Manages git worktrees for parallel agent isolation. Creates isolated worktrees for parallel agents on parallel/{name}-{timestamp} branches, merges results with conflict detection, prunes stale metadata, and reports health status. NOT for user-initiated feature branches — use git worktree directly for that.

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Generate or update docs/project-context.md — the single source of truth for project conventions, tech stack, and anti-patterns. Loaded by all agents as a "constitution" to ensure consistent behavior.

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Fast parallel codebase scouting. Spawns multiple Explore subagents to search directories simultaneously, returning a consolidated file map with architecture fingerprint, complexity estimates, and routing suggestions. Use before planning, debugging, or any task spanning multiple directories. NOT for reading a single known file in depth (use Read directly); NOT for semantic find-usages or go-to-definition.

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Use when running an autonomous multi-hour build of a green-field product — orchestrates planner → contract → generator ⇄ evaluator loop with adaptive scaffolding density per model tier. Triggers on /mk:autobuild, "build me a kanban app", "build a retro game maker", "autonomous build", or any green-field product spec. NOT for scoped single-task work (see mk:cook); NOT for initial project scaffolding only (see mk:bootstrap).

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Structured second-pass reasoning after code review or plan evaluation. Offers named reasoning methods (pre-mortem, inversion, red team, Socratic, etc.) to re-examine findings through a specific lens. Use after /mk:review verdict or any time deeper analysis is needed on an existing output. NOT for initial review (see mk:review); NOT for creating implementation plans (see mk:plan-creator).

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Structured SE task evaluation using 15 benchmark definitions from claude-code-harness research

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Manages shadcn components and projects — adding, searching, fixing, debugging, styling, and composing UI, including chat interfaces. Provides project context, component docs, and usage examples. Applies when working with shadcn/ui, component registries, presets, --preset codes, or any project with a components.json file. Also triggers for "shadcn init", "create an app with --preset", or "switch to --preset".

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Determines if an adolescent meets criteria for initiating sex hormone treatment for gender dysphoria/gender incongruence. Triggered when an adolescent requests sex hormones or presents for gender-affirming hormone therapy evaluation.

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This skill recommends against initiating puberty blocking or gender-affirming hormone treatment in prepubertal children diagnosed with gender dysphoria or gender incongruence. Clinical triggers include a young child presenting with GD/gender incongruence and caregivers or clinicians considering hormone intervention.

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Assists clinicians in determining whether to proceed with social transition for prepubertal youth experiencing gender dysphoria or gender incongruence. Triggers include prepubertal youth with GD/gender incongruence and discussions about initiating social transition.

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Suggests real-time CGM over no CGM for outpatients with type 2 diabetes who use insulin and/or sulfonylureas and are at high risk for hypoglycemia to detect and prevent low glucose events. Consider when initiating CGM in T2D patients on insulin/SU with a history of severe hypoglycemia or impaired awareness of hypoglycemia (IAH).

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This skill guides clinicians to inform and counsel individuals seeking gender-affirming medical treatment about fertility preservation options before initiating puberty suppression in adolescents or before starting hormonal therapy in adolescents and adults. It is triggered when a patient is eligible for pubertal suppression or sex hormone treatment and is about to begin such therapy.

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Calculates initial and escalating dose for pubertal induction hormone therapy based on patient weight or body surface area. Triggers include patient eligible for sex hormone treatment, ready to start hormones.

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Determines whether an adult patient meets eligibility criteria for initiating gender-affirming hormone therapy. Triggered when an adult patient requests gender-affirming hormones or presents for evaluation of hormone therapy eligibility.

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