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概要と使いどころ
Use when building or cleaning the tables and figures for an Academy of Management Journal (AMJ) manuscript — correlation tables, regression/SEM/HLM result tables, the theoretical-model figure, and interaction plots in AOM house style. Finalizes exhibits; it does not run the analysis (amj-data-analysis) or frame the contribution (amj-contribution-framing).
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Mandatory pre-publish review gate for a UGC video render. Transcribes the finished render's AUDIO with Whisper and word-diffs it against the approved spoken script, then gates pinning the final render (video_project_upsert patch.final_render_id) — blocking a render whose generated audio mis-voices a word (e.g. the approved "human-vetted" spoken as "human witted"), says a different number or brand name, flips a negation, drops an approved phrase, or comes back silent. Correct speech written differently ("5mg" said "five milligrams", "30%" said "thirty percent", a spoken URL, "don't" said "do not", "braxleybands" said "braxley bands", a confirmed pronunciation like "AG1" said "A G one") passes. Runnable, gating counterpart to content-goose's review-transcript-integrity atom. Every ugc-video-formats recipe runs this after render and BEFORE pinning the final render.
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Render pixel-accurate Apple Notes (iPhone, light mode) screenshot mockups from a JSON note spec. Outputs HTML + PNG at the iPhone 16/15 Pro native 1180×2556. Supports paragraphs, images, checklists, dividers, autocorrect underline, smart quotes, and an optional iOS keyboard chrome overlay used by the parent video-ad molecule.
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QC gate for a generated static ad image — verify the file opens, matches the requested dimensions, shows the correct product/subject (right shape, colour, label, logo), and has no garbled text or severe artifacts. Records pass/fail/needs-human in verification.md. Used as the final check in the static ad remix flow before shipping.
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Watch a brand's own product footage (screen recording, product film), pick the moment that proves each line with the user, and render those picks as a product layer — free, local. survey.py turns footage into timestamped contact sheets + scene cuts + motion so the agent can actually look at it; the agent writes a cut list (beat → source window + framing); preview.py draws it as a review sheet the user corrects round by round; cut.py renders the approved list into a silent 1080x1920 layer with the creator's area left as a plate. Also frames footage as a filmed screen (keystone, bezel, handheld drift) with dissolves between beats, and takes still screenshots as sources. Use for any format that shows real product footage beside, between or instead of a creator (split-screen, screen inserts, walkthroughs).
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Manage Fabric Warehouse, Lakehouse SQL endpoints, and Mirrored Databases: DDL/DML, COPY INTO, read-only T-SQL, Query Insights diagnostics, and Capacity Metrics CU-spike correlation. Synapse migration target SQL belongs to synapse-migration; Fabric SQL database belongs to sqldb-cli. Triggers: query warehouse, create warehouse table, failed or canceled query, CU spike, Capacity Metrics app, custom SQL pool, Lakehouse table health.
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Brings Azure Monitor, Application Insights, and Log Analytics telemetry into Fabric as Eventhouse external delta tables and correlates it with business data. Use to onboard observability data, judge whether latency or availability affected revenue, or build a Real-Time dashboard and Operations Agent over it.
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Find out why something in a running web app does not work, when the console is empty and the code looks correct. Reads the click, the request, the store and the console together and returns the file:line to open. Use when a button does nothing, a form will not submit, data will not load, a page renders blank or stale, a modal will not close, or the user says "it's broken" and the code review says it is fine.
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Use when SLCI code inspection has failed due to compatibility issues and you need to diagnose the incompatibilities. Traces inspection failures back to root-cause incompatibility settings or known limitations by matching failed code lines against known incorrect code generation patterns and documented limitation scenarios. Hands off to slci-compatibility-analysis for fixes. Trigger keywords: inspect, inspection failed, trace inspection errors, why did inspection fail, SLCI verification failures, limitation.
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 a Simulink model for Simulink Real-Time code generation and deployment. Use when setting up a model for Simulink Real-Time, selecting the correct system target file, fixing TLC/STF mismatches, applying fixed-step solver settings, validating target-platform compatibility, or configuring Simulink Real-Time build options before model build.
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Synthesize new waveforms from scratch for Simulink inports using createInputDataset. Use ONLY when the user asks to generate, create, or synthesize signals (step, ramp, sine, chirp, pulse, noise) to populate a Dataset for External Inputs or Signal Editor. Covers timeseries and timetable formats with correct data type, interpolation, units, and dimensions. Also covers function-call and trigger inport timing setup. Do NOT use when the user wants to load, import, or read existing data from files (MAT, CSV, spreadsheet) — even if that data will be used as model input. Do NOT use for running simulations or plotting outputs.
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Add, configure, and manage faults on Simulink, Simscape, and System Composer model signals for robustness analysis and safety validation. Use when injecting faults (stuck, noise, gain, offset) onto block inports/outports, enabling fault simulation, or analyzing fault effects. Covers sensor failures, signal corruptions, actuator faults, FMEA validation, and robustness testing. Requires Simulink Fault Analyzer.
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Create and maintain AGENTS.md / CLAUDE.md snippet indexes that route tasks to the correct dotnet-skills skills and agents (including compressed Vercel-style indexes).
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Build reactive/event-driven C# with R3 (Cysharp's modern reimplementation of Reactive Extensions). Covers the Observable<T>/Observer<T> model, the OnErrorResume error contract, async dispatch with AwaitOperation, Task/IAsyncEnumerable integration, TimeProvider/FrameProvider scheduling, the concurrency contract, and how R3 differs from System.Reactive (Rx.NET).
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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.
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Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.
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Compare cell-type composition and spatial features across conditions in IMC/MIBI cohorts with the patient as the experimental unit, covering pseudoreplication, per-patient aggregation, mixed models, compositional (Dirichlet/scCODA) differential abundance, diffcyt, per-image-to-patient spatial differential testing (SpaceANOVA), batch covariates, and FDR. Use when testing whether a cell type or spatial niche differs between groups, avoiding cell-level pseudoreplication, choosing a differential-abundance method, or correctly powering an IMC cohort comparison.
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Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedtools genomecov, deepTools bamCoverage/bamCompare/bigwigCompare, bedtools unionbedg, and UCSC bedGraphToBigWig. Covers why a raw coverage bedGraph is not comparable across samples until normalized, the CPM/RPKM/BPM/RPGC normalization menu and the conserved-total assumption that makes them wrong under a global perturbation, the strict sorted-non-overlapping-chrom.sizes bedGraphToBigWig contract that silently corrupts a bigWig, effective-genome-size selection, and bin-size aliasing. Use when building or normalizing a coverage/signal track from a BAM, comparing tracks across samples or conditions, converting bedGraph to a browser-ready bigWig, or diagnosing a track that looks plausible but reports wrong heights.
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Rank and prioritize neoantigen/epitope candidates by likely T-cell response using NeoFox feature annotation, PRIME2.0, BigMHC-IM, the Łuksza/Balachandran fitness model (agretopicity + foreignness), and pVACtools tiering. Encodes the field's hard truths that immunogenicity is the least-solved layer (dedicated scores ~AUROC 0.6-0.7, modest PPV), that scores are valid only for RANKING within one patient (never absolute go/no-go or cross-patient), that DAI has anchor-inflation and WT-denominator traps, and that stacking weak correlated scores into one number is a red flag. Use when ordering a candidate list for a vaccine. Binding lives in mhc-binding-prediction; calling in neoantigen-prediction.
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。
Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.
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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.
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Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.
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。
Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical models. Covers signed-network choice, soft-threshold selection, module preservation, and the marginal-vs-partial-correlation distinction. Use when finding co-expression modules, identifying hub genes, relating gene networks to clinical or experimental traits, or building single-cell co-expression networks. For directed TF-target inference see scenic-regulons and grn-inference; for condition rewiring see differential-networks.
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Compare gene co-expression and regulatory networks between biological conditions to find rewired relationships using DiffCorr, DiffCoEx, DINGO/iDINGO, and CoDiNA. Covers the differential-connectivity-is-not-differential-expression distinction, the pairwise multiple-testing explosion, marginal vs partial (direct) rewiring, and the underpowered-rewiring failure mode. Use when comparing co-expression networks between disease vs control, treatment, or developmental stages, or finding hub genes that rewire without changing mean expression. For single-condition modules see coexpression-networks; for differential expression of means see differential-expression/de-results.
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。