235 件 ・ 関連度順
概要と使いどころ
An overview of the python package for running the GaMMA earthquake phase association algorithm. The algorithm expects phase picks data and station data as input and produces (through unsupervised clustering) earthquake events with source information like earthquake location, origin time and magnitude. The skill explains commonly used functions and the expected input/output format.
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Stress-test a finding against the choices you did not make. Enumerates the discrete forks a competent analyst could have taken (measure definition, sample filter, control set, clustering level, weighting, functional form), runs the specification grid, and reports the distribution rather than a point estimate — then attacks the identifying assumption with named, computable sensitivity statistics. Use when the user says "is this robust", "challenge this result", "specification curve", "multiverse", "how sensitive is this", "what if I'd used a different measure", "stress-test my estimate", or before a result becomes a headline claim. NOT a reviewer of prose or code — it challenges the CLAIM.
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Structured literature search + synthesis with citation extraction, thematic clustering, and gap identification. Use when user says "find papers on X", "do a lit review", "what's the literature on...", "summarize what we know about...", "where's the gap in this field", "review recent work on Y". Produces a written review with BibTeX-ready citations. Uses WebSearch/WebFetch for recent work.
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Compute statistical power, required sample size, and minimum detectable effect (MDE) for a study design, then write a registry-ready power section. Handles two-arm RCTs (with clustering / ICC and unequal allocation), multiple-arm corrections, and a simulation-based power option for non-standard designs (DiD/event-study, IV, panel). Use when user says "power analysis", "power calculation", "MDE", "minimum detectable effect", "how big a sample do I need", "is my study powered", "power for an RCT", or when /preregister needs a power section for an experiment. Produces a power/MDE table, power curves, and a methods paragraph to paste into a preregistration.
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Root-cause a failing or wrong empirical result with a disciplined reproduce → minimise → hypothesise → instrument → fix loop, instead of guessing-and-poking. Use when the user says "why is my regression wrong", "this number changed", "my script errors out", "the result won't reproduce", "debug this", "this estimate looks wrong", or "it worked yesterday". Tuned for research code (R/Stata/Python): type coercion, NA/merge blow-ups, factor levels, clustering/SE choices, weighting, collinearity/convergence, seeds, package-version drift. Use `--no-fix` to localize the root cause without editing shared or load-bearing files.
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Aggregate customer feedback from multiple sources — support tickets, NPS comments, Slack messages, G2 reviews, call transcripts, survey responses — into a unified VoC report with theme clustering, sentiment analysis, trend detection, and actionable recommendations for product, marketing, and CS teams. Chains review-site-scraper for public review data.
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Configure Akka.NET with .NET Aspire for local development and production deployments. Covers actor system setup, clustering, persistence, Akka.Management integration, and Aspire orchestration patterns.
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Quality control for IMC/MIBI data across pixel, channel, image, slide, and batch levels, covering Poisson-count SNR (cell-level Gaussian-mixture and empty-channel comparison), spillover-matrix QC (the three physical sources), drift and the missing EQ-bead analog, acquisition artifacts, and sample-of-origin batch effects. Use when deciding whether to keep or drop a channel, ROI, or slide, distinguishing a dim antibody from a failed one, reading a spillover matrix, or diagnosing batch-driven clustering before analysis.
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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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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.
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Corrects fluorophore spillover (conventional compensation) or spectral overlap (spectral unmixing) and applies variance-stabilizing transforms (logicle/biexponential, arcsinh, log) for flow and mass cytometry. Covers spillover-matrix estimation from single-stain controls, AutoSpill, the spillover spreading matrix and why panel design (not compensation) bounds resolution, compensate-then-transform ordering, and arcsinh cofactor choice (5 for CyTOF, ~150 for fluorescence, per-channel via flowVS). Use when correcting spectral overlap, preparing data for gating/clustering, choosing logicle vs arcsinh, deciding a cofactor, or distinguishing compensation from spectral unmixing.
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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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Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering, and ComplexHeatmap/pheatmap/seaborn rendering. Covers the ward.D vs ward.D2 trap, the row-vs-column scaling decision, multi-track annotations, oncoPrint, and raster rendering for large matrices. Use when visualizing expression patterns across samples or identifying co-regulated clusters.
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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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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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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, MHFP6 LSH forest, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.
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。
Configure Redis for caching and data storage. Set up clustering, persistence, and Sentinel. Use when implementing Redis caching or queues.
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eBay review and feedback authenticity analyzer. Detect fake reviews, suspicious seller feedback patterns, and buyer manipulation. Includes time clustering detection, content similarity analysis, and eBay-specific red flag identification. No API key required.
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Amazon review authenticity analyzer. Detect fake reviews, suspicious patterns, and rating manipulation. Includes time clustering detection, content similarity analysis, rating distribution checks, and verified purchase validation. Progressive analysis with L1-L4 depth levels. No API key required.
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When the user wants to research keywords, find target keywords, or analyze search intent. Also use when the user mentions "keyword research," "keyword tool," "target keywords," "search volume," "search intent," "keyword difficulty," "topical map," "keyword clustering," "People Also Ask," "Google autocomplete," "autocomplete keywords," or "alphabet method." For clusters, use content-strategy.
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。
Run keyword research, classify by search intent, cluster into topical groups, and prioritize for content production. Use this skill whenever the user asks to do keyword research, find target keywords, identify ranking opportunities, classify search intent, build a topical map, or plan a content strategy around what people search for. Triggers on keyword research, keyword strategy, search intent, keyword clustering, topic clusters, keyword difficulty, search volume, ranking opportunity, content gap, what should I write about, target keyword, primary keyword, secondary keyword, long-tail. Also triggers when planning a content calendar or new site without keywords yet defined.
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。
Plan content strategy: content pillars, audience research, topic clustering, funnel mapping, and content audits. Use when deciding what content to create, building a content calendar, planning topic clusters, or finding content gaps.
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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
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。