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Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Nat Commun 12:1302), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.

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Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), TRIBE/HyperTRIBE (ADAR-RBP, A-to-I editing), DART-seq (APOBEC1-YTH for m6A), or Bullseye/SAILOR edit-site detection pipelines. Use when antibody is unavailable or specificity is doubtful, when single-cell RBP profiling is needed (scSTAMP), or when in vivo RBP profiling without UV is preferred.

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Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.

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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.

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CloudBase declarative deployment from a cloudbaserc config (声明式部署, 配置式部署, cloudbaserc 部署) through the deployBuild / deployPlan / deployApply MCP tools. Use when deploying database, functions, app, hosting, or gateway resources described in cloudbaserc.json/yaml as a single desired-state config, when a user wants to build static hosting artifacts locally first (deployBuild), or wants a dry-run plan before applying (deployPlan), or when handling multi-environment deploys via mode / envOverrides. Covers build-plan-apply flow (deployBuild local build → deployPlan dry-run → deployApply confirm=true), hosting build-output neutralization, envId resolution priority, only/skip filtering, concurrency, and continueOnError. Prefer deployBuild (when hosting declares a buildCommand) and deployPlan before deployApply; do not confuse with per-resource tcb CLI deploy or single-function deploy.

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Run a comprehensive on-page SEO audit or optimization pass covering title tags, meta descriptions, header structure, content quality, internal links, image optimization, URL hygiene, and on-page schema. Use this skill whenever the user asks to optimize a page, audit on-page SEO, fix titles or meta tags, review header structure, check internal linking, improve a single URL's search performance, or write SEO-friendly copy. Triggers on on-page SEO, page audit, title tag, meta description, H1, header structure, internal links, image alt, URL slug, page optimization, optimize this page, SEO this page. Also triggers for any single-page review where ranking, click-through, or relevance signal quality is the goal, even if the user does not say 'SEO' explicitly.

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Turn an interpretive-ambiguity audit of a legal text — contract, statute, regulation, or judicial opinion — into a polished deliverable. Produces a multi-page website (default), a single-page interactive site, a Microsoft Word document, a PowerPoint deck, or a LaTeX/PDF. Use whenever a user has a stress-test result, ambiguity audit, or "where will this be litigated" scenarios and wants to publish, present, or share them. Triggers on "publish the audit," "make a report from this," "turn this into a website / deck / brief / Word doc," "make a Netlify site," "build slides of these ambiguities," "render the scenarios," "package this stress test," "produce a LaTeX version," and similar. Pairs with the ambiguity-stress-test skill (the underlying analysis) but works on any structured or semi-structured ambiguity analysis. Visual design is opinionated but the user can override colors, fonts, and brand label. Most formats need Python and a writable filesystem; single-file HTML works where the host has neither.

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Expert patterns for Godot AutoLoad (singleton) architecture including global state management, scene transitions, signal-based communication, dependency injection, autoload initialization order, and anti-patterns to avoid. Use for game managers, save systems, audio controllers, or cross-scene resources. Trigger keywords: AutoLoad, singleton, GameManager, SceneTransitioner, SaveManager, global_state, autoload_order, signal_bus, dependency_injection.

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Expert patterns for adding multiplayer to single-player games including client-server architecture, authoritative server design, MultiplayerSynchronizer, lag compensation (client prediction, server reconciliation), input buffering, and anti-cheat measures. Use when retrofitting multiplayer, porting to online play, or designing networked gameplay. Trigger keywords: MultiplayerPeer, ENetMultiplayerPeer, SceneMultiplayer, MultiplayerSynchronizer, rpc, rpc_id, multiplayer_authority, client_prediction, server_reconciliation, lag_compensation, rollback.

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Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.

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We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positi

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ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).

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Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate

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Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metada

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Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes f

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Crypto market scanner and single-token analyst - movers scans top winners/losers/trending or on-chain runners with pump-risk flags; single-token produces a verdict-first deep report for one token.

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Build a single-product deep-dive showcase page as a self-contained HTML file. Triggers on: "build a product showcase page", "deep dive landing page for [product]", "create a product spotlight page", "product feature page", "single product page", "detailed page about [product]", "build a page showing everything about [product]", "create a long-form product page", "build a sales page for [product]", "product deep dive page", "make a feature breakdown page for [product]".

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Build high-converting affiliate landing pages as single self-contained HTML files. Triggers on: "create a landing page for", "build a landing page", "product landing page", "affiliate landing page", "comparison page for", "vs page", "single product page", "conversion page", "sales page for affiliate", "landing page HTML", "build me a page for", "create a page to promote [product]", "I need a landing page", "make a page for [product]".

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Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.

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Use when a NEW landing page, sales page, or single-product page has to be built — seven-section structure, one page one goal one CTA, copy per block, mobile-first rules, technical and speed requirements, tracking plan, A/B test plan, and a dropshipping single-product mode. Trigger on 'landing page brief', 'build a sales page', 'I need a landing page', 'brief for the dev', 'Shopify product page', 'what should go on the page'. Also use when ad traffic is ready and there is nowhere to send it. Not for — the ad copy pointing at the page, see `05-ad-copy-global`; the offer and its value stack, see `31-offer-design-global`; scoring a finished design, see `47-design-review-global`; coded email, see `49-html-email-template-global`.

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Migrate Infrahub docs feature pages from the legacy topic+guide pair into a cleaner structure (single merged page, hub+spokes, or tutorial extraction). Supports both single-feature migrations (one feature like Profiles or Webhooks) and section-wide migrations (a whole section like Branches & Change Control with multiple features migrated together) when the team has agreed on a section-wide restructure plan. Trigger when the user names a specific feature or section to migrate (e.g. "let's migrate profiles", "start the Resource Manager migration", "do the entire Branches & Change Control section"). Each migration is its own branch off `demo/groups-diataxis-example`, its own PR back to that branch.

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Build cross-platform .NET applications with Uno Platform targeting WebAssembly, iOS, Android, macOS, Linux, and Windows from a single XAML/C# codebase. USE FOR: building cross-platform apps from a single C# and XAML codebase; targeting WebAssembly, iOS, Android, macOS, Linux, and Windows simultaneously; migrating WPF or UWP. DO NOT USE FOR: unrelated stacks; generic tasks that do not need this specific guidance. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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