「tool」の検索結果

A gate before git push / deploy — assembled from your own tools (secret-grep + slop-scan + code-review + build/compile + optional worktree isolation), so AI junk (slop / bugs / secrets / uncompiled code) never reaches a remote or a production server. Turns "I hope it's clean" into a verifiable criterion. Branches: web/OSS (git push/PR) vs deploy-to-server service. Triggers — "check before push", "clean push", "gate before push", "finalize before commit", "run before deploy".

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Security launch audit for a public web app BEFORE you ship or hand it to a client — "vibe coders are getting sued", systematized. An executable pipeline: classify (static / full-stack / AI) → run sections (secrets+supply-chain, DB, auth, infra+headers, legal, LLM/injection) orchestrating deterministic tools + manual checks → GO/NO-GO report. Adapted from Prajwal Tomar's playbook, extended with prompt-injection / supply-chain / secret-history / dependency-CVE layers. NOT the same as pre-push (that = clean push; this = is the product itself safe to launch). Triggers — "security checklist for the site", "audit before launch", "is the site safe", "check before handing to client".

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One-sentence description of what this skill does. Shown as a tooltip on the chip.

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Audit agent runtimes and their tests for lifecycle inference, capability overload, context pollution, correlated verification, prompt-only control, false success, dead compatibility paths, test-only seams, and complexity without contribution. Use for whole-repository agent audits, slop or dead-code triage, test contribution reviews, large refactors, tool/context simplification, and cleanup requests that need proof before deleting code or tests.

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Comprehensive PDF manipulation toolkit for extracting text and tables, creating new PDFs, merging/splitting documents, and handling forms. When Claude needs to fill in a PDF form or programmatically process, generate, or analyze PDF documents at scale.

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GEODE prompt-writing standards. Use when creating or editing runtime prompts, system prompts, tool/developer instructions, model-facing identity text, prompt templates, or scaffold rules that affect model behavior; especially when avoiding identity assertions such as "You are ...".

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Select complementary review lenses for a requested multi-perspective review or a high-risk GEODE change. Covers design, agent constraints, gateway operations, and CLI/tool behavior; not a mandatory four-agent gate for ordinary edits.

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Trigger when: (1) the user mentions "noise", "slop", "frame audit", "video review", "letter spacing", "padding intrusion", "frame extract", "naive arrow", or Korean equivalents (노이즈, slop, 프레임 검수, 글자 깨짐), or (2) after rendering a new or modified Manim scene, or (3) the user asks to review an mp4 in `media/videos/` or `~/Downloads/`. Post-render audit workflow for Manim 1080p60 videos. Extracts keyframes via ffmpeg, inspects them through Claude Code's Read tool, and classifies any defects into four standing categories (naive arrow / padding intrusion / glyph kerning drift / frame-order error). Catalogues 12+ verified incidents across the four GEODE scenes so each is caught the first time, not rediscovered. The companion authoring skill is [[manim-scene-craft]].

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Scope, preregister, execute, audit, normalize, and publish GEODE evaluations with research-question, reproduction, attempt-lineage, trajectory, verifier-receipt, and immutable artifact contracts. Use for benchmark runs or comparisons, eval-artifact and cache-accounting audits, GPT or subscription result normalization, research question or hypothesis framing, retry diagnosis, trajectory publication, DPO or reward-data readiness reviews, and requests involving MCPMark, tau2, BFCL, Agent-World, HAL, Terminal-Bench, or Toolathlon.

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Converts XLSX spreadsheets, including multi-sheet workbooks, into CSV files that can be read and grepped directly. Use whenever an .xlsx report needs processing — exports from Xero, Cryptio, bank statements, or any tool that delivers spreadsheet output.

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Makes the agent reconsider a task it just handed back to the human and find a way to do it itself, checking memory, CLI tools, skills, MCP servers, and documentation in turn. Use when the user invokes `/you` or `$you`, or replies that the agent should do something itself rather than asking them.

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Triages an already-dirty Git working tree: breaks down every uncommitted change hunk by hunk, separates deliberate edits from tool-written churn, possibly accidental reversions, misplaced scope, and sensitive content, asks the user about the ambiguous cases, and proposes an ordered set of commits plus a list of hunks to hold back. Use when the user invokes `/pc` or `$pc`, asks what they should commit, wants their uncommitted changes broken down, or wants commits proposed for a dirty working tree or pile of accumulated local modifications. To plan commit boundaries for a change before or while implementing it, use `incremental-commits` instead.

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Adds or changes allowed commands in AI agent permission configs for OpenCode and Claude Code. Use when a command needs adding to an agent's allow list, when permission settings for existing commands need changing, when setting up a new AI tool that requires command permissions, or when the user asks to stop being prompted for a particular command.

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Trae a este proyecto las mejoras que la plantilla de origen recibió después de la instanciación — lee .template-origin, calcula el diff del tooling (skills, hooks, scripts, workflows) contra la plantilla actual y propone aplicarlo. Úsalo cuando la persona quiera actualizar/sincronizar el proyecto con la plantilla (p. ej. "actualiza la plantilla", "trae las mejoras nuevas del template").

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Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL, Stockholm) and re-encode FASTQ quality offsets using Biopython Bio.SeqIO. Use when changing a file format for a downstream tool, fixing FASTQ quality encoding (Phred+33 vs Phred+64 vs Solexa), or when a conversion risks silently dropping annotations or quality scores.

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Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical models. Covers signed-network choice, soft-threshold selection, module preservation, and the marginal-vs-partial-correlation distinction. Use when finding co-expression modules, identifying hub genes, relating gene networks to clinical or experimental traits, or building single-cell co-expression networks. For directed TF-target inference see scenic-regulons and grn-inference; for condition rewiring see differential-networks.

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Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and tissue-of-origin from plasma WGS. Centers on the nuclease-footprint reframe (every feature re-reads one nucleosome object), the mandatory GC correction, and the cross-protocol non-comparability that breaks naive classifiers. Runs FinaleToolkit (real CLI/Python, MIT) and the Griffin Snakemake pipeline; DELFI is a method, not a package. Use when deriving fragment-based signal from cfDNA, choosing a feature family for detection vs subtyping, or diagnosing why a fragmentomic model failed validation.

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Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.

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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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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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Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and translates calls into WHO GLASS reporting categories. Use when screening clinical or surveillance isolates for AMR, distinguishing acquired vs intrinsic vs point-mutation resistance, calling rpoB / katG / pncA / gyrA / mgrB mutations, reconciling AMRFinderPlus vs RGI vs ResFinder disagreement, contextualising carbapenemases or mcr alleles on plasmids, predicting susceptibility from genotype against the WHO Mtb 2nd-edition catalogue, or building a hAMRonized multi-lab AMR surveillance pipeline.

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Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.

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Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

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Plot per-gene mutation distributions on a protein-domain map (lollipop / needle plots) showing mutation position, recurrence count, and variant classification with maftools, g3-lollipop, trackViewer, and ProteinPaint. Use when visualizing recurrent mutation hotspots on a single gene's protein, marking domain boundaries from UniProt/Pfam, comparing missense vs truncating distributions, or contrasting two cohorts on the same lollipop.

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。