73건 · 관련도순
Redesign a lesson to centre students' cultural backgrounds, community knowledge, and lived experience. Use when making curriculum relevant and inclusive for diverse student populations.
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treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data to find robust and interpretable associations between cell subsets and patient clinical end points. These associations are aimed to recapitulate the nested proportions prevalent in workflows inovlving manual gating, which are often overlooked in workflows using automatic clustering to identify cell populations. We developed treekoR to: Derive a hierarchical tree structure of cell clusters; qua
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MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide
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Assesses genetic health of populations for conservation using effective population size estimation (GONE2 for recent Ne trajectory, NeEstimator for contemporary Ne, Stairway Plot 2 and PSMC for historical Ne), F-statistics (hierfstat), runs of homozygosity (detectRUNS), and genetic diversity metrics. Use when estimating effective population size, detecting inbreeding or bottlenecks, or assessing genetic diversity in threatened species from microsatellite or SNP data.
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Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.
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Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering to avoid artificial cell populations. Use when identifying and removing doublets from scRNA-seq data.
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Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without predefined gates.
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Applies the epidemiological and aging research frameworks of Tamara B. Harris (epidemiologist, National Institutes of Health). Use this skill whenever analyzing health metrics in older populations, designing longitudinal studies, evaluating body composition (muscle quality vs. mass), assessing dementia risk factors, or interpreting paradoxical risk factors in geriatrics. Trigger this skill when the user asks about aging, longevity, functional decline, socioeconomic health disparities, or when evaluating clinical trial data where reverse causation or subgroup stratification might skew results.
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Applies the epidemiological reasoning and population-health frameworks of Albert Hofman (Harvard epidemiologist, Rotterdam Study). Trigger this skill whenever you are analyzing public health strategies, preventive medicine, cohort study design, cardiovascular or neurodegenerative disease risks, or healthy aging. Use it when evaluating whether to use population-wide interventions versus individual screening, assessing risk factors in elderly populations, or tracing adult chronic diseases back to early-life or fetal origins.
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Redesign a lesson to centre students' cultural backgrounds, community knowledge, and lived experience. Use when making curriculum relevant and inclusive for diverse student populations.
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Somatic movement and whole-body retraining as Joseph Pilates designed it in the Contrology method and as Moshé Feldenkrais designed it in Awareness Through Movement and Functional Integration, with enough cross-reference to the broader somatics landscape (Alexander Technique, Hanna Somatics, Body-Mind Centering) that an agent can place a user into the right method. Covers the Pilates reformer and mat system, the six Pilates principles, the Feldenkrais ATM lesson structure, the nervous-system learning frame that distinguishes somatics from exercise, and the safety posture that matters for rehab populations. Use for queries about core training, rehab-adjacent movement, chronic pain patterns, and learning-based movement re-education.
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Use this skill when a periodic user access review is due, an auditor asked for access review evidence, or someone says "prepare the access review", "run the quarterly user recertification", "who still has admin", "check leavers still have access", "build the access review sheets for managers" or "our last review was a rubber stamp". Picks the systems in scope, builds account populations reconciled against HR, pre-flags leavers, orphans, shared and dormant accounts, assigns independent reviewers, defines the decisions to record, and plans the removal follow-up.
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Comprehensive K-12 or higher-ed system analysis: predict student dropout risk with early warning indicators, optimize curriculum alignment and pacing, personalize learning paths for at-risk and diverse populations, and audit school operations for resource efficiency..
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Digital equity and trauma-informed design for marginalized populations. Activate on "accessibility", "offline-first", "trauma-informed", "reentry", "recovery population", "shared device", "unstable phone", "digital equity", "design justice", "low-literacy", "intermittent access". NOT for general UX, marketing optimization, or enterprise SaaS design.
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Task-sized forensic analysis of Vivado synthesis and routed timing evidence for processor RTL. Use when Codex must trace a named setup or hold path, audit whole-design timing populations, compare implementation runs, map primitive, LUT, CARRY, BRAM, DSP, MUXF, register, and routed-net stages back to Chisel or generated RTL, distinguish logic from routing pressure, identify missing DCP queries, or write an evidence-backed timing report. This skill is read-only by default and stops at ranked modification directions. Use optimize-chisel-fpga-timing for RTL edits and routed A/B implementation closure.
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Handle ethical requirements, IRB approval, trial registration, and pre-analysis plans for RCTs. Use when user mentions: research ethics, IRB, informed consent, trial registration, pre-analysis plan, PAP, data security, vulnerable populations, research transparency.
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Unsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSOM, PhenoGraph, FlowSOM-via-CATALYST, with UMAP/tSNE for visualization. Covers the type-vs-state marker distinction (cluster on lineage, test state within clusters), over-provision-then-metacluster, the Weber-Robinson benchmark, seed dependence and metacluster stability, why embeddings are for looking not measuring, and median-heatmap annotation/merging. Use when discovering populations without predefined gates, choosing a clustering algorithm, selecting the number of metaclusters, or annotating clusters into cell types.
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Detects and removes doublets/aggregates from flow, spectral, and mass cytometry before clustering or quantification. Covers FSC-A vs FSC-H singlet discrimination (the Area-Height non-proportionality, not a 1D area gate), FSC-W/SSC width gating, CyTOF Gaussian discrimination parameters (Center/Offset/Width/Residual/Event_length) and DNA intercalator gating, and the residual heterotypic conjugates that survive scatter gating and masquerade as double-positive populations. Use when filtering aggregates before phenotyping, choosing a doublet method for flow vs CyTOF, or diagnosing a suspicious double-positive cluster.
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Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and reproducible automated gating (openCyto gating templates, flowDensity data-driven thresholds, flowClust model-based gates), organized as a hierarchical GatingSet (flowWorkspace) and round-tripped with FlowJo via CytoML. Covers the canonical gate order (time -> debris -> singlets -> live -> lineage), FMO-vs-isotype boundary setting, gate-order dependence and recompute semantics, rare-event/MRD gating, and per-population statistics. Use when building a gating strategy, automating a manual FlowJo scheme across samples, choosing manual vs data-driven gates, or extracting population frequencies.
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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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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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Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Than 2008) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use when testing inter-species gene flow, dating admixture events, identifying introgressed segments, building phylogenetic networks for reticulate evolution, or applying the ABBAclustering (Koppetsch-Malinsky-Matschiner 2024) framework for divergent-species gene flow.
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Prepares statistical reports for clinical trials following CONSORT 2025, SPIRIT 2025, ICH E9(R1) estimands, and FDA 2023 covariate adjustment guidance. Covers Table 1 generation, analysis populations (ITT/FAS/PP/Safety), the 5 ICH E9(R1) intercurrent-event strategies, MMRM under MAR (mmrm), reference-based MI (rbmi J2R/CR/CIR), Permutt tipping-point sensitivity, and Rubin's-rules vs frequentist variance debate. Use when preparing regulatory submissions, defining estimands, or implementing missing-data sensitivity analyses.
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Complete bedside prescribing reference for Mirago (mirabegron, beta-3 adrenoceptor agonist) for overactive bladder — covering contraindications, safety screening, drug interactions, dose selection in special populations, titration, and administration. Use when a clinician asks how to start mirabegron, what dose to use in renal or hepatic impairment, is mirabegron safe in this patient, mirabegron drug interactions, or Mirago for OAB.
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