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Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS. Handles silent-miscounting traps (featureCounts -p v2.0.2 API break, STAR strandedness column choice, salmon NumReads-sum without tximport, RSEM non-integer expected_count, GENCODE _PAR_Y suffix, zero-length-transcript TPM divide-by-zero), and encodes the tximport countsFromAbundance decision tree with the "lengthScaledTPM is not TPM" warning. Use when assembling a gene-by-sample count matrix from aligner or quantifier output, importing salmon/kallisto for DESeq2 vs limma-voom, choosing strandedness column for STAR, debugging zero-count panics, or building tx2gene mapping.

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。

Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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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.

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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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Improve Coval trace quality after basic ingestion works. Use when traces are sparse, missing useful STT/LLM/TTS/tool spans, missing attributes needed for Coval built-in metrics, or when a customer wants maximum debugging and observability value from agent traces.

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。

Retrieve and analyze simulation results from a Coval run. Use when user wants to review evaluation outcomes or debug agent behavior.

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。

Dense UI posture — maximum information density with clear hierarchy. Use when building or reworking admin dashboards, data tables and grids, ops or monitoring views, settings-heavy panels, debug inspectors, state or log viewers, and multi-pane tool UIs someone drives all day.

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。

Overlay controller for dialogs, sheets, modals, windows, and toasts opened by dispatch. Use when opening, adding, registering, or debugging an overlay, or touching features/overlays/**, app/DeferredSingletonCore.tsx, lib/redux/slices/overlaySlice.ts, dispatch(openOverlay(...)), useOpenX hooks, or XController components. NOT for the WindowPanel component itself (use window-panels).

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。

The cross-repo scheduling system (sch_* tables, matrx-scheduler). Use when touching features/scheduling/**, /schedules or /administration/scheduling, migrations/sch_*.sql, a scheduled agent, cron, trigger, lease, or claim, or debugging ghost tasks, missed fires, double-runs, or stuck claims.

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。

The matrx-frontend side of the matrx-extend Chrome extension bridge. Use when adding or changing a FRONTEND_RPC action handler, a window-panels deep-link the extension opens, a headless API route it calls, or debugging a silent chrome.runtime.sendMessage or Broadcast round-trip. NOT for code in matrx-extend, matrx-local, or aidream (each has its own connect-* skill).

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。

Find and identify the CCSNavArea_IsValidNavMesh function in CS2 server binary using IDA Pro MCP. Use this skill when reverse engineering CS2 server.dll or libserver.so to locate the nav-mesh validity predicate. It is a tiny non-virtual-looking helper that returns `g_pNavMesh != nullptr` (15 bytes), referenced only from a vtable slot, with no debug string of its own. Emits a unique IDA-style byte signature and a func YAML. Mirrors the find-CCSNavArea_IsValidNavMesh.py preprocessor (xref_gvs g_pNavMesh intersected with the tail signature `48 83 38 ? 0F 95 C0 C3`). Trigger: CCSNavArea_IsValidNavMesh, IsValidNavMesh, g_pNavMesh predicate

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。

Find and identify the CCSGameRules::TerminateRound function in the CS2 server binary using IDA Pro MCP. Use this skill when reverse engineering CS2 server.dll or libserver.so to locate the round-end-processing function by finding the code that references both the bare "TerminateRound" debug tag string and the "TerminateRound: unknown round end ID %i\n" warning-format string — both are referenced from the same function. Trigger: CCSGameRules_TerminateRound

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。

Find and identify the CCSGameRules_ResetRound function in CS2 server binary using IDA Pro MCP. Use this skill when reverse engineering CS2 server.dll or libserver.so to locate the round-reset routine. It is the only function that references the "GMR_ResetRound\n" debug log string, and is the predecessor anchor for find-CCSGameRules_PostCleanUp (which it calls). Emits a unique IDA-style byte signature and a func YAML. Mirrors the find-CCSGameRules_ResetRound.py preprocessor (xref_strings "GMR_ResetRound\n"). Trigger: CCSGameRules_ResetRound, ResetRound, GMR_ResetRound

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。

Perform language and framework specific security best-practice reviews and suggest improvements. Use when the user explicitly requests security best practices guidance, a security review/report, or secure-by-default coding help. Trigger only for supported languages (python, javascript/typescript, go), and not for general debugging or non-security 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。

Manages shadcn components and projects — adding, searching, fixing, debugging, styling, and composing UI. Provides project context, component docs, and usage examples. Applies when working with shadcn/ui, component registries, presets, --preset codes, or any project with a components.json file. Also triggers for "shadcn init", "create an app with --preset", or "switch to --preset".

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Guide for when to use and when not to use return validators in Convex functions. Use this skill whenever the user is writing Convex queries, mutations, or actions and needs guidance on return value validation. Also trigger when the user asks about Convex type safety, runtime validation, AI-generated Convex code, Convex AI rules, Convex security best practices, or when they're debugging return type issues in Convex functions. Trigger this skill when users mention "validators", "returns", "return type", or "exact types" in the context of Convex development. Also trigger when writing or reviewing Convex AI rules or prompts that instruct LLMs how to write Convex code.

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。

Five Whys root cause analysis. Iteratively asks "why" to drill past symptoms to underlying causes. Use for debugging, investigating failures, or understanding why something went wrong.

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[30] ANALYZE. Understand how changes impact the system — what's the core, what's affected, what depends on what. Use when planning changes, analyzing systems, debugging issues, or anytime you need to see the full picture of cause and effect. Triggers on "what's affected", "impact analysis", "dependencies", "scope mapping", or when you need to understand ripple effects.

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[31] ANALYZE. Universal deep thinking methodology for any situation requiring quality reasoning. Use when solving problems, debugging, making decisions, analyzing code, planning, reviewing, or anytime you need thorough thinking instead of surface-level responses. Triggers on "think deeply", "analyze thoroughly", "reason carefully", "deep thinking", "understand completely", or any task requiring careful thought.

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。

Sentry error tracking and monitoring for OneKey. Use when configuring Sentry, filtering errors, analyzing crash reports, or debugging production issues. Covers platform-specific setup (desktop/mobile/web/extension) and error filtering strategies.

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Develops iOS/iPhone applications with XcodeGen, SwiftUI, and SPM. Triggers on XcodeGen project.yml configuration, SPM dependency issues, device deployment problems, code signing errors, camera/AVFoundation capture debugging, iOS version compatibility, or "Library not loaded @rpath" framework errors. Use when building iOS apps, fixing Xcode build failures, or deploying to real devices. Not for AVPlayer playback issues (seek/scrub/frame stepping → avfoundation-reference skill).

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 operational modes (brainstorm, implement, debug, review, teach, ship, orchestrate). Use to adapt behavior based on task type.

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。

Systematically finds and fixes bugs using proven debugging techniques. Traces from symptoms to root cause, implements fixes, and prevents regression.

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。