'dating' 검색 결과

Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM architecture (ADSL, BDS, OCCDS, ADTTE) with traceability, treatment-emergent AE conventions, baseline derivation, SUPPQUAL/NSV handling, Define-XML 2.1, and Pinnacle 21 / CORE validation. Use when working with clinical trial datasets in CDISC SDTM/ADaM format, preparing analysis-ready data, or validating for regulatory submission.

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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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Detect and adjust for horizontal pleiotropy in two-sample Mendelian randomization by distinguishing uncorrelated (UHP) from correlated (CHP) pleiotropy and choosing among Egger, MR-PRESSO, MR-RAPS, CAUSE, LHC-MR, LCV, MR-Clust, MR-Mix, and contamination-mixture methods. Use when validating an MR causal claim, running the STROBE-MR sensitivity battery, suspecting a shared heritable confounder, working under weak-instrument or polygenic-exposure regimes, or reconciling discordant estimates across robust methods.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/SUPPA2/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.

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Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.

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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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Manage feature manifests for code traceability. Use when creating new features, updating existing features, checking feature health, or exploring the feature-to-code relationship. Activates for manifest validation, feature creation, changelog updates, and traceability queries.

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Refute-before-prove research discipline: automated counterexample sweeps before any formalization, meter-integrity audits for information-bound experiments, mutation-tested model checkers, pre-registered commit-or-cut gates for speculative directions, wrong-turn reporting, and numeric-claim provenance. Use when validating any new theorem, bound, equilibrium, or security claim; when building or trusting a checker, simulator, or experiment; or when deciding whether a speculative research direction lives or dies. NOT for exploratory brainstorming, product prioritization, writing style, or literature review.

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Operations, debugging, and optimization for DAG workflows. Performs root cause analysis on failures, profiles execution performance, aggregates results from parallel branches, bridges context between nodes, and learns patterns from execution history. Activate on "DAG failed", "why did it fail", "root cause", "performance profile", "aggregate results", "merge branches", "execution patterns", "optimize DAG". NOT for planning DAGs (use dag-planner), executing DAGs (use dag-runtime), or validating outputs (use dag-quality).

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Design a normalized, machine-readable "work receipt" that answers what changed, why, by whom, and with what validation, for any AI-coding-agent task regardless of backend (Claude Code, Codex, Cursor, Aider, CI, or homegrown). Use when defining a receipt schema, normalizing heterogeneous agent logs into one evidence shape, gating PR merges on artifact-backed proof, or designing an OSS maintainer's fast-reject/fast-merge workflow. NOT for validating a DAG node's output against its own schema (use output-contract-enforcer), continuous runtime monitoring of a live coordination daemon (use runtime-verification-for-agents), or general Port Daddy claims/notes/salvage mechanics (use port-daddy-agent-skill).

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Author a pull request an AI coding agent can actually get merged: a scoped, coherent diff; a Summary and Test Plan backed by real evidence; correct triage of required-and-blocking CI gates versus external/advisory checks (e.g. a Cloudflare Pages preview build); draft-while-WIP discipline; named fixup commits for real review findings; and a clean landing through a merge queue without force-pushing or bypassing branch protection. Use when opening, updating, triaging red CI on, or landing an agent-authored GitHub PR. NOT for this repo's internal release ceremony, actor embodiments, or contributor mirror-sync mechanics (use port-daddy-internal-dev), tracking backlog/issue lifecycle across a board (use agent-issue-tracker-workflow), or deciding what to build next / sequencing a roadmap (use legible-roadmap-with-sidequests).

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Recipe for creating or changing a floating window. Use when adding a window, deleting, killing or retiring a window or overlay ('kill this panel', 'remove the X window', consolidating X into Y and deleting X), editing a window component, declaring restore or ephemeral behavior, wiring a ?panels= link or the Tools grid, or a window fails to restore after reload. NOT for drag/resize/tray internals (use window-panels) or for opening an overlay (use overlay-system).

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The procedure for every doc change in common-docs or a repo's CLAUDE.md, FEATURE.md or SKILL.md. Use when creating, editing, moving or deleting a doc, finding duplicate or disagreeing docs, planting a repo pointer, consolidating a node, or on /docs and the daily docs-steward run.

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Convert an existing find-XXXX SKILL.md into a preprocessor Python script, updating configs/<GAMEVER>.yaml and removing the old SKILL.md. Covers xref-string-based and LLM_DECOMPILE-based discovery patterns.

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Create a new cpp_tests entry for validating a C++ interface vtable layout against binary reference YAMLs. Creates the .cpp test file in cpp_tests/ and appends a configs/<GAMEVER>.yaml entry under cpp_tests:. Use when a user asks to add vtable layout validation for a new hl2sdk_cs2 interface class.

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This skill should be used when the user wants to "investigate a bug", "debug an issue", "figure out why something is happening", "find the root cause", "troubleshoot", "強い推論で調査", "仮説を立てて検証", "原因を特定", "バグの原因調査", "なぜ動かないか調べて", "問題を切り分け", "原因不明", "デバッグ", or mentions systematic hypothesis-driven debugging. NOTE: Use this for investigating UNKNOWN causes, not for validating design proposals (use devils-advocate for that).

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This skill should be used when the user wants to "stress-test a design", "challenge an idea", "red team a proposal", "get critical feedback on a design", "validate a design", "adversarial architecture review", "risk assessment", "設計を検証して", "反論をもらいたい", "設計を批判的にレビュー", "デビルズアドボケート", "ストレステスト", "弱点を指摘して", "穴を見つけて", "この設計で良いか", "リスク評価", "設計のアーキテクチャレビュー", or mentions structured adversarial review of a proposal or design. NOTE: Use this for validating PROPOSALS and DESIGNS through adversarial debate, NOT for generic code review, PR review, or normal review requests (use /codex:review or /codex:adversarial-review for those). Also NOT for investigating unknown bugs (use /agent-dialectics:strong-inference for that).

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Align explicit requirements, implicit expectations, non-goals, observable acceptance, evidence, and decision authority before OpenSpec specs and executable tasks finalize. Use when authoring or updating a proposal, design, specs, or tasks, or when a request hides a material product choice. Do not use for routine implementation of an already-authorized task, unrelated conversation, or facts the repository can answer.

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Use when adding or updating Spark AI provider models or their compact and preflight metrics, especially baidu-oneapi, Grok, Claude, GPT, DeepSeek, OneAPI, context windows, output budgets, prices, thinking maps, or transports.

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Integrate and maintain Robelest Convex Auth in apps by always checking upstream before implementation. Use when adding auth setup, updating auth wiring, migrating between upstream patterns, or troubleshooting @robelest/convex-auth behavior across projects.

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