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概要と使いどころ
Finds Fabric items across every workspace with the Catalog Search API when the workspace is unknown, locating an item by display name, inventorying one item type tenant-wide, and returning the workspace and item IDs later calls need. Dataflow Gen1 and Gen2 items are not supported. Use only to locate items; once found, query them with the owning item skill such as sqldw-cli, spark-cli, eventhouse-cli or fabriciq.
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Local vision CLIs: glance (describe/ask/OCR an image), ground (locate a target, pixel box), detect (element inventory), trace (image to SVG geometry), crop (cut a pixel box to a file), and scripts/html_shot.py (HTML file to image). Use for any task involving an image — questions, text, splitting and transcribing long screenshots or chat histories, locating elements, comparing, rebuilding as HTML/SVG, digitizing a sketch or diagram, reading values off a chart, operating a GUI from screenshots — and to re-check an image yourself when a description you were given lacks a detail.
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Entity Framework Core best practices including NoTracking by default, query splitting for navigation collections, migration management, dedicated migration services, and common pitfalls to avoid.
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Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and Oxford Nanopore (cDNA/direct-RNA) long reads, using the isoseq+pigeon pipeline, SQANTI3, and ONT tools (IsoQuant, FLAIR, Bambu, StringTie2). Covers why a novel isoform is an artifact until proven otherwise (RT template-switching, intra-priming, and 5' degradation manufacture junctions and truncations), the SQANTI3 structural categories and their trust order, the Kinnex skera-split step, orthogonal CAGE/poly-A/short-read-junction validation, and why long-read isoform quantification needs EM. Use when building a full-length isoform catalog, classifying/filtering long-read transcripts, running Iso-Seq or ONT cDNA/dRNA analysis, or judging novel-isoform reliability.
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Designs cytosine (CBE, C-to-T) and adenine (ABE, A-to-G) base-editor guides by positioning the target base at the activity-peak of the editing window (protospacer positions ~5-7, PAM-distal numbering), minimizing bystander edits for product purity, reading dinucleotide context (APOBEC1 TC favored / GC disfavored), and selecting the editor variant (BE4max, ABEmax, ABE8e, YE1/SECURE, TadCBE, CGBE, SpG/SpRY-BE). Covers knockout by premature stop (CRISPR-STOP/iSTOP) and splice-site disruption, the three off-target classes (Cas-dependent, Cas-independent DNA, RNA), outcome prediction (BE-Hive/DeepBE), and the base-vs-prime-vs-HDR decision. Use when installing a transition mutation without a double-strand break, knocking out a gene without indels, or choosing CBE vs ABE. Generic guide scoring, prime editing, and HDR donors are separate skills.
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Calls significant loops from protein-directed and targeted 3C assays (HiChIP, PLAC-seq, Capture Hi-C/PCHi-C, ChIA-PET) where the contact background is peak-anchored and coverage-biased, so generic Hi-C loop callers (cooltools dots, Juicer HiCCUPS) use the wrong null. Covers FitHiChIP (config-driven coverage+distance-decay spline regression, peak-to-peak vs peak-to-all foreground, loose vs stringent background, coverage vs ICE bias), MAPS (positive Poisson regression on bias factors for PLAC-seq/HiChIP), hichipper (restriction-site-distance bias model + library QC), CHiCAGO (Delaporte two-component Brownian+technical background for asymmetric bait x other-end Capture Hi-C), the with/without separate-ChIP anchor decision, and differential loops via diffloop. Use when calling loops from HiChIP/PLAC-seq/Capture Hi-C, choosing FitHiChIP/MAPS/CHiCAGO, picking peak-to-all vs peak-to-peak, setting the loop FDR, supplying ChIP peaks as anchors, QCing a HiChIP library, or comparing loops between conditions.
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Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.
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Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE DESeq), LRT reduced-model rules, the interaction-term resultsNames trap, continuous-covariate scaling and splines, repeated measures via duplicateCorrelation or dream, high-cardinality categorical pseudo-singular designs, sample swap detection via XIST/RPS4Y1 expression and somalier/NGSCheckMate genotypes, SABV (sex-as-biological-variable) mandate, Simpson's-paradox collapsing of technical replicates, and the `~ 0 + group` parameterization for clean contrasts. Use when building a design matrix, troubleshooting reversed fold-change direction, encoding paired or repeated-measures designs, detecting sample swaps, deciding sex-as-covariate, or aggregating technical replicates.
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Delimits putative species boundaries from molecular data within the de Queiroz 2007 unified-lineage framework using ASAP (Puillandre 2021 successor to ABGD), mPTP C++ (Kapli 2017 successor to bPTP; bPTP is Python NOT R), GMYC single/multi-threshold (Pons 2006; Fujisawa 2013), multilocus BPP v4 with prior calibration from data (NOT defaults; Yang 2015), SNAPP + BFD* for SNP delimitation, DELINEATE (Sukumaran 2021) speciation-process modeling to address Sukumaran & Knowles 2017 PNAS critique that MSC delimits structure not species, integrative-taxonomy congruence (Padial 2010; Carstens 2013), Dsuite for introgression testing before sister claims (Malinsky 2021), and Meyer & Paulay 2005 barcoding-gap-absence caveat. Use when delineating species from DNA barcoding data, resolving cryptic complexes, choosing among ASAP/mPTP/BPP/DELINEATE, calibrating BPP priors, distinguishing introgression from ILS, or applying the Sukumaran-Knowles oversplitting correction.
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Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-element bead normalization of instrument sensitivity drift (CATALYST normCytof, premessa), and reference-anchor cross-batch normalization (CytoNorm, per-cluster quantile splines). Covers the distinction between within-run drift correction and between-batch correction, the mandatory anchor/reference sample, why normalization is per-cluster with many quantiles, and the over-correction risk. Use when correcting CyTOF signal drift, harmonizing multi-batch or multi-site studies, or deciding whether to normalize data versus model batch in the design.
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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.
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Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.
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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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Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, calibration (Platt, isotonic), feature importance (SHAP, atomic attribution), and prospective validation. Use when building target-specific predictive models from in-house bioassay data, ADMET endpoints, or selectivity profiles.
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Calls HLA class I and class II alleles at 2/4/6/8-field resolution from WGS/WES/RNA-seq/long-read data using OptiType, HLA-LA, T1K, Polysolver, HLA-HD, arcasHLA, StarPhase, or HIBAG imputation. Use when typing for HSCT, solid-organ transplant, neoantigen prediction, PGx screening (B*57:01, B*15:02, etc.), or disease-association studies, with reconciliation across tools and IPD-IMGT/HLA version mismatch handling.
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Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.
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Use when working with ANY GPU rendering, Metal, OpenGL migration, shaders, 3D content, RealityKit, AR, USD/USDZ files, or display performance. Covers Metal migration, shader conversion, RealityKit ECS, RealityView, USDKit, ProMotion.
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Implement SwiftUI navigation patterns including NavigationStack, NavigationSplitView, sheet presentation, tab-based navigation, and deep linking. Use when building push navigation, programmatic routing, multi-column layouts, modal sheets, tab bars, universal links, or custom URL scheme handling.
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Fetch WeatherKit current, minute, hourly, and daily forecasts; weather alerts; iOS 18+ changes, historical comparisons, summaries, and statistics; and required Apple Weather attribution. Use when integrating weather data, showing forecasts or alerts, caching WeatherKit responses, displaying attribution, or reviewing WeatherKit query limits in iOS apps.
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Implement, review, or improve photo picking, camera capture, and media handling in iOS apps using PhotoKit and AVFoundation. Use when working with PhotosPicker, PHPickerViewController, camera capture sessions (AVCaptureSession), photo library access, image loading and display, video recording, or media permissions. Also use when selecting photos from the library, taking pictures, recording video, processing images, or handling photo/camera privacy permissions in Swift apps.
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Implement and review Apple TipKit feature-discovery UI for iOS 17+ apps. Use when adding or auditing in-app tips, contextual help, coach marks, Tip, TipView, popoverTip, rules, events, actions, display frequency, testing overrides, reusable tip identifiers, or iOS 18+ TipGroup and CloudKit tip sync; avoid for generic SwiftUI navigation or layout outside tip presentation.
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Display and manipulate PDF documents using PDFKit. Use when embedding PDFView to show PDF files, creating or modifying PDFDocument instances, adding annotations (highlights, notes, signature widgets), extracting text with PDFSelection, navigating pages, generating thumbnails, filling PDF forms, or wrapping PDFView in SwiftUI.
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Build CarPlay-enabled apps using the CarPlay framework. Use when creating navigation, audio, communication, EV charging, parking, or food ordering apps for the car display, working with CPTemplateApplicationScene, CPInterfaceController template hierarchies, CPListTemplate, CPMapTemplate, CPNowPlayingTemplate, configuring CarPlay entitlements, or integrating with CarPlay Simulator for testing.
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Create media playback experiences using AVKit. Use when adding video players with AVPlayerViewController, enabling Picture-in-Picture, routing media with AirPlay, using SwiftUI VideoPlayer views, configuring transport controls, displaying subtitles and closed captions, or integrating AVFoundation playback with system UI.
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。