「cluster」の検索結果

Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (log2 IP/input bigWig via deepTools bamCompare; pyGenomeTracks; Gviz; IGV/UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), feature-distribution stacked bars, and volcano/MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012; Meyer 2012). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features, generating DRACH motif logos as sanity checks, rendering volcano plots of differential m6A, or reproducing the stop-codon enrichment plot.

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Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.

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Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.

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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 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 differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity matrices for clustering, classifying archaea, evaluating MAG (metagenome-assembled genome) species assignment, applying skani for fast metagenomic ANI screening, or reconciling 16S rRNA-based taxonomy with whole-genome ANI.

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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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Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. Use when normalizing variant identifiers, joining variant databases by cluster ID, or tracking deprecated rsIDs through historical merges.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract) with SES scaling, k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

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Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose skills based on what they actually do. Requires the screenpipe daemon (https://github.com/screenpipe/screenpipe) running locally on port 3030 — the skill has no other data source and will refuse to run if screenpipe is unreachable. All detection runs locally; only redacted cluster summaries reach the LLM.

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Bootstrap the central system spec at `docs/system/` for a repository that has never had one. Scans the governed surface, proposes a concept map clustered by directory, and materializes elements + shards ONLY after a human confirms that map. Use when adopting the baseline on an existing project, or when the corpus needs re-deriving from scratch. Re-runnable. Requires `memory.architecture_map.enabled` and a declared `governed_surface`.

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Monitor DX clusters for rare station spots, track active DX expeditions, and get daily band activity digests.

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Biblioteca do Facebook para busca eficiente de similaridade e clustering de vetores densos. Suporta bilhões de vetores, aceleração GPU e vários tipos de índice (Flat, IVF, HNSW). Use para busca k-NN rápida, recuperação de vetores em larga escala ou quando você precisa de busca pura de similaridade sem metadados. Melhor para aplicações de alto desempenho.

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Banco de dados de embeddings de código aberto para aplicações de IA. Armazene embeddings e metadados, realize buscas vetoriais e full-text, filtre por metadados. API simples com 4 funções. Escala de notebooks para clusters de produção. Use para busca semântica, aplicações RAG ou recuperação de documentos. Melhor para desenvolvimento local e projetos de código aberto.

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Instâncias GPU em nuvem reservadas e sob demanda para treinamento e inferência de ML. Use quando você precisar de instâncias GPU dedicadas com acesso SSH simples, sistemas de arquivos persistentes ou clusters multi-node de alto desempenho para treinamento em larga escala.

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Orquestração de treinamento distribuído em clusters. Escala PyTorch/TensorFlow/HuggingFace do laptop para milhares de nós. Ajuste de hiperparâmetros integrado com Ray Tune, tolerância a falhas, escalabilidade elástica. Use ao treinar modelos massivos em múltiplas máquinas ou executar varreduras distribuídas de hiperparâmetros.

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Process the batch of incoming Bridge Classroom feedback. Pull open `classroom-feedback` issues from the PBS repo, cluster them by defect class, verify each against the actual board, and fix at the right altitude — patch a single board, or (when a class recurs) build a gate, sweep the whole corpus, and regenerate/drop collectively. Engine bugs route to the Classroom repo; bridge-judgment calls go to Rick. Nothing leaves the machine without David's OK. Invoke as `/issue` (optionally with an issue number or scenario to restrict the run).

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Produce a weekly digest of what Ahmad saved in OpenMark over a given time window, clustered by topic. Use whenever Ahmad asks "what did I save this week", "what's new in OpenMark", "last week's saves", "this week's bookmarks", "what happened in my feed", "weekly recap", or any temporal summary of saved content. Faster than full newsletter — output is a scannable digest, not a published post. Triggers on "this week", "last week", "what's new", "weekly digest", "recent saves", "recap".

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Plan, create, and configure production-ready Azure Kubernetes Service (AKS) clusters. Covers Day-0 checklist, SKU selection (Automatic vs Standard), networking options (private API server, Azure CNI Overlay, egress configuration), security, and operations (autoscaling, upgrade strategy, cost anal...

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Identify poisoned training data and backdoored models across the ML pipeline.

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Find over-permissive RBAC roles and service-account token abuse paths in Kubernetes using kubectl auth can-i, rbac-police, kubectl-who-can, and rakkess during authorized cluster security reviews.

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Run CIS Kubernetes Benchmark checks and remediate findings with kube-bench.

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Apply bottom-up and top-down role mining techniques to discover optimal RBAC roles from existing user-permission assignments, reducing role explosion and enforcing least privilege.

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