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概要と使いどころ
Write, review, or audit this repository's technical documentation, including README.md, CONTRIBUTING.md, root and scoped AGENTS.md files, docs pages, and documentation drift. Use for source-backed documentation authoring, behavior verification, and cross-surface consistency. Do not use for code review, deslop diff cleanup, or whole-page rewrites, splits, or reorganizations handled by docs-refactor.
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。
Refactor a whole documentation page in this repository without losing source-verified behavior facts. Use for page rewrites, splits, reorganizations, or substantial shortening of README sections, docs pages, or instruction files. Do not use for ordinary documentation authoring, targeted corrections, or documentation review; use technical-documentation instead.
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。
Capture Unity Editor windows or Game View rendering as PNG. Use for visual checks, debugging, documentation, or annotated UI element coordinates.
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。
Read this when you need Chrome MV3-shaped APIs — bookmarks, tabs, windows, history, downloads, or top sites — in standalone OmOWright.
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。
Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.
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。
Designs cytosine (CBE, C-to-T) and adenine (ABE, A-to-G) base-editor guides by positioning the target base at the activity-peak of the editing window (protospacer positions ~5-7, PAM-distal numbering), minimizing bystander edits for product purity, reading dinucleotide context (APOBEC1 TC favored / GC disfavored), and selecting the editor variant (BE4max, ABEmax, ABE8e, YE1/SECURE, TadCBE, CGBE, SpG/SpRY-BE). Covers knockout by premature stop (CRISPR-STOP/iSTOP) and splice-site disruption, the three off-target classes (Cas-dependent, Cas-independent DNA, RNA), outcome prediction (BE-Hive/DeepBE), and the base-vs-prime-vs-HDR decision. Use when installing a transition mutation without a double-strand break, knocking out a gene without indels, or choosing CBE vs ABE. Generic guide scoring, prime editing, and HDR donors are separate skills.
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。
Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046), MeTPeak (HMM over sliding windows; Cui 2016 *Bioinformatics* 32:i378), MACS3 / MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment confirmation via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output formats, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union; cross-caller IDR-equivalent), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody-based methods cannot resolve, and orthogonal-validation routes (miCLIP / GLORI / m6A-SAC-seq / m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set as a whole, reconciling differing peak sets across tools, validating MeRIP peaks against orthogonal single-base methods, interpreting peaks at the 5' end where m6Am contamination is possible, or recommending a multi-tool consensus strategy.
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。
Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.
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。
Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.
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。
Designs pooled sgRNA libraries for CRISPR knockout, interference (CRISPRi), activation (CRISPRa), Cas12a multiplex, base-editor, and prime-editor screens. Covers on-target scoring (Rule Set 2, Azimuth, DeepSpCas9, CRISPRon), off-target scoring (CFD, MIT), TSS-relative positioning for CRISPRi/a (Horlbeck, Dolcetto, Calabrese), PAM-variant chemistries, control-guide composition, oligo cloning architecture, and library QC. Use when choosing a genome-wide library (GeCKOv2 vs Avana vs Brunello vs TKOv3 vs Inzolia), designing a focused or paralog-focused custom library, picking CRISPRi vs CRISPRa TSS windows, deciding control-guide proportions, or diagnosing library skew and dropout in a freshly cloned pool.
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。
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.
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。
Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.
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。
Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.
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。
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.
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。
Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CTCF-only/DNase-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.
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。
Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.
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 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.
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。
Validates animation durations, enforces typography scale, checks component accessibility, and prevents layout anti-patterns in Tailwind CSS projects. Use when building UI components, reviewing CSS utilities, styling React views, or enforcing design consistency.
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。
Expert security auditor for AI Skills and Bundles. Performs non-intrusive static analysis to identify malicious patterns, data leaks, system stability risks, and obfuscated payloads across Windows, macOS, Linux/Unix, and Mobile (Android/iOS).
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。
Memory is the cornerstone of intelligent agents. Without it, every interaction starts from zero. This skill covers the architecture of agent memory: short-term (context window), long-term (vector stores), and the cognitive architectures that organize them.
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。
Generate production-ready Next.js/React components from design specifications. Use this skill when you have a design specification document and need to create React/TypeScript components with Tailwind CSS styling, Vitest tests, and Storybook documentation.
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。
Migration guide for Swift and iOS. Use when migrating ObservableObject to @Observable (iOS 17), enabling Swift 6/6.2 Strict Concurrency, fixing @MainActor/Sendable warnings, adopting Approachable Concurrency (Swift 6.2), or handling iPadOS 26 windowing system changes (UIRequiresFullScreen deprecation). Covers breaking changes and version upgrade tasks.
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。
Weekly sweep of ALL transcript-bearing spoken events (earnings calls, conference firesides, CMDs, investor days, AGMs, investor updates) for every active thesis, via the Quartr watchlist. Produces a triage digest in Daily Intel/ flagging thesis-touching mentions and recommending deep reads. Use when user says "event sweep", "what did my companies say this week", "conference sweep", or on the weekly schedule. Also `--setup` (build/rebuild the Quartr watchlist from active theses) and `[N]` (window override in days, default 8).
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。
Generate a backward-looking retrospective of vault activity (addressed callouts + Log entries) over a time window (1w / 1m / 1q), overlay with newsflow + earnings transcripts + price action, and rank trade ideas by the gap between official narrative and market reaction. Output is an immutable Research note. Use when user says "retro", "retrospective", "what did I do this week/month/quarter", "review activity against market", or "recommend trades from recent research".
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。