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Evaluate and install ecosystem tools (Hermes plugins, skills, integrations) — assess complexity vs. benefit before installation, show examples for visual tools, and avoid "cloned but not configured" states.
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Generate a plan for how an agent should accomplish a complex coding task. Use when a user asks for a plan, and optionally when they want to save, find, read, update, or delete plan files in $CODEX_HOME/plans (default ~/.codex/plans).
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A six-year-old code reviewer who asks "why?" about everything. Catches over-engineering, confusing names, and unnecessary complexity. Output is a 1-2 line summary of the request as a whole: how is the file? Is the class nice? Is the function correct?
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You are an expert software engineer and systems analyst. Use when user asks "how does X work" with expectation of depth, user wants to understand a complex system spanning many files, or user asks for architectural analysis or pattern investigation.
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No-code automation democratizes workflow building. Zapier and Make (formerly Integromat) let non-developers automate business processes without writing code. But no-code doesn't mean no-complexity - these platforms have their own patterns, pitfalls, and breaking points. This skill covers when to use which platform, how to build reliable automations, and when to graduate to code-based solutions. Key insight: Zapier optimizes for simplicity and integrations (7000+ apps), Make optimizes for power
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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scaling; MetaPlotR; deepTools `computeMatrix scale-regions`), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (bigWig of log2 IP/input via deepTools `bamCompare`; ggcoverage; pyGenomeTracks; Gviz; IGV / UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), 5'UTR / CDS / 3'UTR stacked-bar feature-distribution summaries, and volcano / MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012 *Nature* 485:201; Meyer 2012 *Cell* 149:1635 — concurrent founding papers from different labs both showed this independently). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features for figure 1, generating DRACH motif logos as sanity checks on the peak set, rendering volcano plots of differential m6A, or reproducing the Dominissini 2012 / Meyer 2012 stop-codon enrichment plot.
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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot with 5'UTR / CDS / 3'UTR scaling; MetaPlotR; deepTools `computeMatrix scale-regions`), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (bigWig of log2 IP/input via deepTools `bamCompare`; ggcoverage; pyGenomeTracks; Gviz; IGV / UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), 5'UTR / CDS / 3'UTR stacked-bar feature-distribution summaries, and volcano / MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012 *Nature* 485:201; Meyer 2012 *Cell* 149:1635 — concurrent founding papers from different labs both showed this independently). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features for figure 1, generating DRACH motif logos as sanity checks on the peak set, rendering volcano plots of differential m6A, or reproducing the Dominissini 2012 / Meyer 2012 stop-codon enrichment plot.
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[40] PLAN. Create clear action plans with steps, success criteria, and risk awareness. Use before implementing features, making changes, starting projects, or anytime you need a roadmap to success. Triggers on "plan this", "how should we approach", "what's the strategy", "steps to complete", or when facing complex multi-step work.
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Use this skill for internal TypeScript work in the nuxt-ui-tools repository. Covers the repository's inference-first style, forbidden escape hatches, public API typing rules, schema-driven type design, and how to keep complex types powerful without making the codebase harder to maintain.
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