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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue), MMSplice (modular per-region CNN with calibrated ΔPSI), SpliceTransformer/TrASPr (tissue-aware transformers), SpliceVault (empirical 300K-RNA lookup of likely mis-splicing outcomes), CADD-Splice (composite score). Applies the ClinGen SVI 2023 framework for ACMG/AMP variant interpretation (PVS1, PP3, BP4 evidence codes), HGVS splicing nomenclature (c.123+1G>A, c.123-3T>G, r.spl?), extended-window scoring for deep-intronic pseudoexons, tissue-specific predictions, branchpoint variant detection (BPHunter, LaBranchoR), and splice-switching ASO design. Use when interpreting splice impact of clinical variants, prioritizing VUS, identifying deep-intronic pathogenic variants, or designing ASOs.

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Azure Machine Learning SDK v2 for Python. Use for ML workspaces, jobs, models, datasets, compute, and pipelines.

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AI-powered E2E web testing — eyes and hands for AI coding tools. Declarative YAML scenarios, Playwright execution, visual matching (OpenCV + OCR), platform auto-detection (Flutter/React/Vue), learning DB. Install: npx skills add ksgisang/awt-skill --skill awt -g

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AI and machine learning workflow covering LLM application development, RAG implementation, agent architecture, ML pipelines, and AI-powered features.

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Synchronize recent research learnings across all affected theses, sector notes, and macro documents. Use after a research session or when user says "sync", "propagate", or "update everything".

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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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YC Office Hours — two modes. Startup mode: six forcing questions that expose demand reality, status quo, desperate specificity, narrowest wedge, observation, and future-fit. Builder mode: design thinking brainstorming for side projects, hackathons, learning, and open source. Saves a design doc. Use when asked to "brainstorm this", "I have an idea", "help me think through this", "office hours", or "is this worth building". Proactively invoke this skill (do NOT answer directly) when the user describes a new product idea, asks whether something is worth building, wants to think through design decisions for something that doesn't exist yet, or is exploring a concept before any code is written. Use before /plan-ceo-review or /plan-eng-review. (gstack)

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Route communication modes, learning workflows, retrospectives, output discipline, and perspective shifts to focused productivity skills.

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Write or revise AI-learning-notes article pages in "寫文章模式" when the user asks for articles, technical articles, blog posts, bilingual versions, article formatting consistency, shared article-base alignment, responsive layout, summary/TOC decisions, contrast, or publishing-flow compatibility.

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Promote project-specific memories into strict, small global memory only when they are cross-project, stable, useful, safe, and worth the global context cost. Load when the user says make this global, remember across projects, save this globally, or promote this learning.

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Capture durable project memory from work, debates, debugging discoveries, learned conventions, deferred options, and session outcomes. Load when the user says remember this, save this learning, record what happened, update project memory, or preserve context for future agents.

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Capture actionable learnings that emerge during conversation — when the agent or user discovers that a skill, a set of skills, or a process needs to be updated based on what's happening in the current chat. Sub-skill of the learn-from orchestrator. Load when the user says "we should update the skill for this", "this should be a skill rule", "add this as a gotcha", "the skill should know about this", "update the process for this", "remember this for next time", "this is important for the skill". Also triggers when the agent notices a skill's guidance was wrong or incomplete, a process step failed or was unnecessary, a new pattern emerged, a guardrail was missing, a workaround became a pattern, or a debugging session reveals a gap.

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Instrument a shipped product's AI agents with tracing and observability so you can see what they did, why outputs happened, and what each run cost. Plain-language primer plus free-tier-first backend selection (Langfuse, Phoenix, LangSmith, Braintrust) and OpenTelemetry/OpenInference instrumentation. Load when the user asks to add observability, add tracing, instrument my agents, see what my agent is doing in production, set up Langfuse or Phoenix or LangSmith, debug why my agent gave a bad answer, or track LLM cost per request. Also fires when agent-system-architecture or setup-evaluation requires an observability plan for an agent-chain product. NOT for tracing the coding agent itself — that is run-trace. Precondition for runtime-learning-loop.

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Analyse experiment results, run validity checks (SRM, exposure parity, data integrity, novelty/primacy), interpret causally, make a ship/iterate/kill decision against the pre-declared rule, and append to cumulative learnings. Forces honest readouts — strips significance claims from underpowered or peek-violating tests; never lets directional results masquerade as causal wins. Load when results exist, or when the user says "read out this experiment", "analyse the test", "did the test win", "interpret the results", "what did we learn", "ship or kill", or when the experimentation orchestrator routes here.

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Analyzes your recent Codex chat history to identify coding patterns, development gaps, and areas for improvement, curates relevant learning resources from HackerNews, and automatically sends a personalized growth report to your Slack DMs.

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Development skill from everything-claude-code

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Azure Machine Learning SDK v2 for Python. Use for ML workspaces, jobs, models, datasets, compute, and pipelines.

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。

AI-powered E2E web testing — eyes and hands for AI coding tools. Declarative YAML scenarios, Playwright execution, visual matching (OpenCV + OCR), platform auto-detection (Flutter/React/Vue), learning DB. Install: npx skills add ksgisang/awt-skill --skill awt -g

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。

AI and machine learning workflow covering LLM application development, RAG implementation, agent architecture, ML pipelines, and AI-powered features.

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。

Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.

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Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

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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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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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