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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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Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indicator species (indicspecies IndVal.g group-equalized), PERMANOVA paired MANDATORILY with PERMDISP (Anderson & Walsh 2013; dispersion confounds centroid tests), Joint Species Distribution Models (HMSC, sjSDM, gjam) with explicit rejection of "residual covariance equals biotic interaction", phylogenetic community ecology (SES_MPD/MNTD), trait-environment via RLQ + fourth-corner with corrected modeltype=6 (Dray 2014), bipartite network metrics (NODF, modularity) with curveball null (Strona 2014), and Mantel-test replacements (dbRDA, GDM) for spatial data. Use when testing how environmental gradients structure communities, identifying habitat indicator taxa, partitioning variance among predictors, deciding whether PERMANOVA significance is location vs dispersion, picking among HMSC/sjSDM/gjam, or replacing Mantel tests for landscape data.

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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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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.

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Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and when to defect to de novo computation.

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Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/SUPPA2/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.

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Understand how a confirmed vulnerability in an owned system is triggered so you can patch and test it. This is not exploit development for offense. No payloads, malware, or attack procedures.

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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.

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Use this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations as PowerPoint (.pptx) files; reading, parsing, or extracting text from any .pptx or .potx file (even if the extracted content will be used elsewhere, like in an email, summary, or creating a different type of slide deck); editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates (.potx), layouts, speaker notes, or comments. Trigger whenever the user asks for a PowerPoint or .pptx file, or references a .pptx or .potx filename, regardless of what they plan to do with the content afterward. However, when the user asks for a deck, slides, a slide deck, or a presentation without naming a file format, default to using a dedicated slide-deck artifact type or a separate slides skill if this session offers one; otherwise, use this skill.

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docs (editable docs people share and comment on; the default for any document, named as a doc or not: a document, report, proposal, resume, cover letter, letter, contract, policy, form, template, worksheet, essay, handbook, guide, how-to, cheat sheet, SOP or other writing to keep, share, collaborate on, send, submit, print or sign; a doc exports to Word, PDF, Markdown or Google Docs, so needing a file to send, attach, upload, submit or print is no reason to pick Word, and a file nobody asked for is a doc, not Word; a plan, comparison, summary or notes asked in chat stays in chat; a pasted claude.ai artifact link may be a doc: check with docs tools first; Word or another file format named, tracked changes wanted, or a .docx to change or use as a template → that format's skill): making one → if no docs-connector instructions are in context, call its `guide` (topic.instructions) first; then create the doc (headings only, no body) before any search, file read or plan, even with files attached.

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Sync the current machine's configuration into the dotfiles repo and update the React showcase page. Use this skill whenever the user says "sync dotfiles", "update dotfiles", "sync config", "actualizar dotfiles", "sincronizar config", "update the repo with my current setup", or anything about pulling their current machine state into the dotfiles repo. Also trigger when the user mentions updating the toolkit page, adding new tools to the page, syncing Claude Code or Codex config (AGENTS.md, codex agents/skills/hooks), or keeping the dotfiles repo in sync with what's actually installed.

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Read this before the first Google Drive, Docs, Sheets or Slides connector call whenever the task creates or changes a Google file. Use this skill whenever the user wants to create or change a Google Doc, Sheet or Slides file in their Google Drive. Triggers include: a request that names Google Docs, Sheets, Slides or Drive and asks to make, edit, format, copy or rename a file; a docs.google.com link with a request to change that file, even a one-line fix or suggested edits; and any follow-up change to a Google file from earlier in the chat, even "change it" or "add a tab". Includes helper scripts for document positions, cell ranges and slide layout. However, if the user asks for a doc, deck or spreadsheet without naming Google, or gives a Google file only as source material for something new, use Claude's own output type instead. Do NOT use for read-only questions about a Google file, or for Word, Excel, PowerPoint or PDF files.

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Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx) or Word templates (.dotx). Triggers include: any mention of Microsoft Word Documents, such as 'Word doc', 'word document', '.docx', '.dotx', 'microsoft doc'. Also use when extracting or reorganizing content from .docx or .dotx files, inserting or replacing images in documents, find-and-replace in Word files, working with tracked changes or comments, or converting content into a polished Word document. If the user asks for a deliverable as a Word or .docx file (to download, email or print), use this skill. However, if they ask for a document, page, report, memo, or notes WITHOUT naming a file format and the session offers Claude's own dedicated document or page skill or connector, use that instead, even if they will email or print it. Do NOT use for PDFs, spreadsheets, Google Docs, or coding unrelated to document generation.

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Reconstruct workflow behind a past coding-agent artifact using local ax sessions/commits/skills/tool traces. Use when asked how X was built.

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Tools are how AI agents interact with the world. A well-designed tool is the difference between an agent that works and one that hallucinates, fails silently, or costs 10x more tokens than necessary. This skill covers tool design from schema to error handling.

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Show specification status and progress

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Single-track / single-episode music-player mockup template — glassmorphic iOS-Music style player card with ambient album-art wash, for showcasing one song, one podcast episode, or one audio jingle as a shareable interactive surface.

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Build premium scroll-driven web pages and product showcases inspired by high-end app, hardware, and product interaction patterns. Use for Raycast-like, Apple-like, NVIDIA-like, RTX/GPU, SaaS, AI browser, parallax, sticky scroll, pinned reveal, Three.js GLB model, Web Audio sound effect, responsive accessibility, and performance-safe frontend requests.

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Generate a single-file product landing page with a layered ASCII cosmos hero (rotating ASCII planet, drifting irregular asteroids, comet trails, nebula gas clouds — each in its own harmonious color) plus full marketing sections (about / features grid / showcase / spec / pricing / CTA / footer). Takes a natural-language description of one product (any kind — a note app, a coffee subscription, a CLI tool, an indie hardware, a hosting service…) and outputs ONE working .html file with deep-space dark or warm-letterpress theme. Runs in BOTH Claude Code (writes to ~/Desktop) and GLM / online chat (outputs HTML inline). Trigger phrases: "做个宇宙风产品落地页", "生成 ASCII 产品官网", "ascii-cosmos-gen ...", "做个独立软件 / 独立硬件落地页", or when user drags this skill folder into chat asking for an atmospheric product landing page.

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Generate and safely advance the SDD Composy task projection from approved PRD, stories, and TechSpec: import contracts, list/next/show, and guarded start/block/transition/verify. Use when work must be decomposed or a task's state inspected or moved — 'quebrar a spec em tarefas', 'listar as tarefas', 'qual a próxima task', 'mark TASK-003 blocked'. Do NOT use to implement a task (sdd- execute), reconcile Markdown and JSON (sdd-sync), or for a status overview (sdd- status).

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Use when starting any conversation in a repository that uses PWDEV Power - establishes how to find and apply Power skills before any response, including clarifying questions

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Curate durable PWDEV Flow project decisions, lessons, and conventions. Use when the user asks to capture, list, show, link, supersede, or select project memory, or when an approved workflow decision should persist across phases.

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