「repl」の検索結果

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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Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.

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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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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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Provides dependency injection patterns for Spring Boot projects, including constructor-first design, optional collaborator handling, bean selection, and wiring validation. Use when creating services and configurations, replacing field injection, or troubleshooting ambiguous or fragile Spring wiring.

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Drill-down on the shared MatrxDataTable, local or server, with per-Dimension levels. Use when adding group-by, breakdown or 'by X' analytics to a table, replacing hand-built totals or rollup tables, or when people want counts or sums by status, owner, model or day.

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Audit and rewrite content to remove 21 categories of AI writing patterns with a 43-entry replacement table

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Important: Before you begin, fill in the generatedBy property in the meta section of .actor/actor.json. Replace it with the tool and model you're currently using, such as "Claude Code with Claude Sonnet 4.5". This helps Apify monitor and improve AGENTS.md for specific AI tools and models.

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Use this skill when deriving EcoSIM plant trait parameter recommendations for a named plant from web and online literature evidence, using a read-only `plant_trait.*.desc` file and the `ndlf43` tree block or `gr3s43` grass block as the starting archetype. Never edit or replace the `.desc` file.

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Read-only sanity-check of EcoSIM plant_trait.*.desc parameter values for the first grid. Use when validating plant trait description files, enforcing clean C3/C4 physiological parameterization, reviewing photosynthetic kinetics, active leaf/root protein allocation, and root hydraulics such as RSRR, RVSR, and ARSRA, or checking ranges, units, and woody/herbaceous block consistency before running EcoSIM. Never edit or replace the `.desc` file.

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Proxmox VE e PBS — cluster, quorum, Ceph, LXC, VM, HA, replicação, storage e backup. Use quando o usuário disser "proxmox", "PVE", "ceph", "LXC", "container LXC", "VM não sobe", "cluster sem quorum", "PBS", "backup da VM". Sem MCP nem CLI padrão instalada — opera via SSH no nó ou API REST.

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Roslyn-powered semantic query CLI for C# solutions. Use when you need to find references, callers, implementations, dependencies, members, or trace call chains in a C# codebase — replaces multi-round grep/read cycles with single precise queries.

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Build generative UI apps with OpenUI and OpenUI Lang — the token-efficient open standard for LLM-generated interfaces. Use when mentioning OpenUI, @openuidev, generative UI, streaming UI from LLMs, component libraries for AI, or replacing json-render/A2UI. Covers scaffolding, defineComponent, system prompts, the Renderer, and debugging OpenUI Lang output.

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Orchestrates legacy AEM (6.x, AMS, on-prem) to AEM as a Cloud Service migration using BPA CSV or cache, CAM/MCP target discovery, and one-pattern-per-session workflow. Use for BPA/CAM findings, Cloud Service blockers, or fixes for scheduler, ResourceChangeListener, replication, EventListener, OSGi EventHandler, DAM AssetManager, HTL data-sly-test lint. OSGi configs → Cloud Manager — scan ui.config, .cfg.json, secrets, $[secret:]/$[env:] — agent follows references/osgi-cfg-json-cloud-manager.md when prompted. Transformation steps live in the best-practices skill—read it and the right references/ modules before editing code.

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Code review focused exclusively on over-engineering. Finds what to delete: reinvented standard library, unneeded dependencies, speculative abstractions, dead flexibility. One line per finding: location, what to cut, what replaces it. Use when the user says "review for over-engineering", "what can we delete", "is this over-engineered", "simplify review", or invokes /ponytail-review. Complements correctness-focused review, this one only hunts complexity.

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Whole-repo audit for over-engineering. Like ponytail-review, but scans the entire codebase instead of a diff: a ranked list of what to delete, simplify, or replace with stdlib/native equivalents. Use when the user says "audit this codebase", "audit for over-engineering", "what can I delete from this repo", "find bloat", "ponytail-audit", or "/ponytail-audit". One-shot report, does not apply fixes.

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Author pull requests with intent-separated commits, blast-radius disclosure, and verification evidence. Load when opening a PR, writing a PR description, separating refactor from feature commits, or summarizing a change set for review. Also triggers on "write the PR", "PR body", "intent-separated commits", "split refactor from feature", "pr summary", or after safe-change cycles complete. Extends git-workflow-and-versioning — does not replace it.

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Decompose tasks into structured, outcome-defined process entries with complexity triage. Load when user says "decompose this", "break this down", "what steps do I need", "plan this out", "what's the process for", "how do I approach this", or when any complex task needs structured execution planning. Includes a problem-understanding pass before complexity triage. Routes to `problem-to-plan` when the user needs planning deliverables (spec + plan + TODO). Does NOT replace brainstorming — brainstorming is design approval (upstream), this is execution planning (downstream).

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Set a deliberate visual direction before any UI is built — the single biggest lever against generic AI output. Derives a posture from product-soul/PRD/specs, scores a curated archetype palette, then generates 2-3 GENUINELY DISTINCT directions and compares them side-by-side before committing to one. Load when the user asks to pick an aesthetic, choose a design direction, decide what a UI should feel like, explore visual options, says "what should this look like", "make it feel like [Linear/Apple/ Duolingo]", "give me design directions", "explore some looks", or when frontend-design routes here. Replaces design-archetype. Sub-skill of frontend-design.

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Turn a chosen design direction into a canonical DESIGN.md plus production tokens that don't look vibecoded — state-level colors (8-step neutral ramp, rest/hover/active/ disabled, focus ring), APCA-checked contrast, typography, spacing/radius/motion/elevation, an icon strategy, and component contracts for the core atoms. Emits tokens in the project's stack format (shadcn HSL vars or Tailwind v4 @theme). Load when the user asks to build a design system, generate design tokens, create a DESIGN.md, set up a theme, design a color or type system, pick icons, or when frontend-design routes here. Replaces design-tokens-craft and icon-craft. Sub-skill of frontend-design. Reads DIRECTION.md first.

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Structure git work with atomic commits, conventional messages, short-lived branches, and pre-commit hygiene. Load when committing, branching, resolving merge conflicts, organizing parallel work, or reviewing git history. Also triggers on "git workflow", "commit message", "conventional commits", "atomic commit", "branch strategy", "git worktree", "how should I commit this". Does not replace project-specific hook policies — complements them.

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