Results for “apply”

Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.

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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 (Solis-Lemus 2017) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012; Lipson 2013). 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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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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Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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Constructs and validates polygenic risk scores using LDpred2-auto, SBayesRC, MegaPRS, PRS-CS, PROSPER, MUSSEL, BridgePRS, JointPRS, PRSmix, or PGS Catalog Calculator with ancestry-aware reference panels (HapMap3, UKB-LD), Pejaver-style calibration, and PRS-RS reporting standards. Use when computing PRS for cohorts, applying Whiffin-style absolute-risk transformation, assessing cross-ancestry portability (Martin 2017 / Ding 2023 continuous ancestry), or auditing PRS manuscripts against the 22-item PRS-RS reviewer checklist.

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Map N6-methyladenosine (m6A) RNA modifications at single-nucleotide resolution using miCLIP (Linder 2015), miCLIP2 + m6Aboost machine learning (Kortel 2021), GLORI (Liu 2023, antibody-free chemical conversion), DART-seq (Meyer 2019, APOBEC1-YTH fusion), m6Anet (nanopore direct RNA), or MeRIP-seq with calibration. Use when distinguishing antibody-based from antibody-free m6A detection methods, applying the DRACH motif constraint, reconciling cross-method disagreements (DART 44% in DRACH vs GLORI), or detecting m6Am at the cap.

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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2025 Nat Genet; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

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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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Iteratively detects and auto-fixes technical debt in a codebase using three quality criteria from debt-analysis references: conditional branch simplification, encapsulation, and separation of concerns. Applies fixes directly to code, runs existing tests to verify no regressions, re-analyzes, and loops until all high-severity issues are resolved or max iterations (5) reached. Use this skill when you want to automatically improve code quality with real code changes, reduce technical debt systematically, or clean up code to meet quality standards. Trigger on phrases like "fix technical debt", "clean up code quality", "refactor and fix issues", "improve code quality automatically", "apply debt fixes", "fix code problems", "eliminate debt".

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Triage GitHub issues by applying type, effort, priority, and area labels. Runs in an isolated context to avoid polluting the main conversation with issue details. Delegates to a specialized triage agent with label validation hooks.

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Initialize or resume the SDD Composy workspace of a repository: preview missing governance and OKF bundle files, apply only approved absent paths, persist the artifact language, and verify. Use when a project needs SDD set up or resumed — 'inicializar o SDD', 'configurar o workspace SDD', 'run init first', or when any SDD skill returned not_initialized. Do NOT use for generic CLAUDE.md or repository setup outside SDD Composy, or for other plugins' init.

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Reconcile SDD Composy task Markdown and the JSON projection: read-only inspect and plan, then apply only with an explicit authority and the CONFIRM-SDD-SYNC token. Use when task contracts and operational state diverged — 'sincronizar as tarefas', 'o JSON das tasks está desatualizado', 'markdown and json disagree'. Do NOT use to list or advance tasks (sdd-tasks), for a status overview (sdd-status), or to simulate approval.

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Use when starting any conversation in a repository that uses PWDEV Power - establishes how to find and apply Power skills before any response, including clarifying questions

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Analyze a completed phase diff for high-confidence behavior-preserving simplifications and apply only explicitly approved proposals. Use after execution and before review to reduce duplication, dead code, needless complexity, or avoidable inefficiency.

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Diagnóstico e operação de Kubernetes — pods, deployments, ingress, HPA, PVC, StorageClass, NetworkPolicy, Secrets, Helm, ArgoCD, cert-manager. Use quando o usuário disser "kubernetes", "k8s", "pod", "deployment", "ingress", "CrashLoopBackOff", "não sobe", "escalar", "helm", "argocd". Leitura livre; apply, scale, delete passam pelo portão.

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Format Haskell source files: *.hs, *.lhs, and *.hsig, with the project's configured formatter: fourmolu, ormolu, or stylish-haskell. Use before compiling, after source edits, and when applying project style.

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Apply continuous improvement principles to iteratively enhance processes, code quality, team practices, and system performance through small, incremental changes. Use when improving development processes, optimizing workflows, reducing waste, enhancing code quality over time, implementing retrospective learnings, or fostering a culture of continuous improvement.

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When the user wants to apply psychological principles, mental models, or behavioral science to marketing. Also use when the user mentions 'psychology,' 'mental models,' 'cognitive bias,' 'persuasion,' 'behavioral science,' 'why people buy,' 'decision-making,' 'consumer behavior,' 'anchoring,' 'social proof,' 'scarcity,' 'loss aversion,' 'framing,' or 'nudge.' Use this whenever someone wants to understand or leverage how people think and make decisions in a marketing context.

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Apply DESIGN, canon, and modules to every page in the inventory, producing a deployable static HTML site. Three render branches (approved page, template-applied sibling, unique render). Per-page, incremental, idempotent, content-preserving by default.

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Apply a Content Driven Development process to AEM Edge Delivery Services development. Use for ALL code changes - new blocks, block modifications, CSS styling, bug fixes, core functionality (scripts.js, styles, etc.), or any JavaScript/CSS work that needs validation.

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[BETA] Expert assistance for the Adobe I/O CLI plugin `@adobe/aio-cli-plugin-aem-rde` — the `aio aem rde` / `aio aem:rde` command tree used to deploy, inspect, log-tail, snapshot, and troubleshoot AEM Rapid Development Environments (RDEs). Activate ONLY when the user explicitly references RDE concepts: 'AEM RDE', 'Rapid Development Environment', `aio aem rde`, `aio aem:rde`, `aem-rde`, RDE snapshots, RDE deploy/install, `rde install`, `rde inspect`, `rde status`, `rde history`, `rde reset`, the `@adobe/aio-cli-plugin-aem-rde` package, or Cloud Manager program/environment configuration that is specifically for an RDE environment. Do NOT activate on generic AEMaaCS phrases like 'deploy to AEM Cloud', 'push my bundle', 'tail the publish log', 'cloud sandbox', or unqualified 'dispatcher-config / frontend / env-config deployments' — those belong to Cloud Manager pipelines, not RDE. This skill is in beta. Verify all outputs before applying them to production projects.

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Guides Rust performance optimization. Use when profiling, benchmarking, reducing allocations, improving cache locality, choosing between rayon/async/threads, or applying SIMD/parallelism.

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