Docs & Writing

stanfish06 Bundle

Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.

deadmade Skill

Fan out N parallel workers, drain them, and return one report. Use for /swarm, 'swarm this', or parallel coverage, races, gauntlets, and exploration.

stanfish06 Bundle

Use this skill when the user wants a .pptx with smooth cross-slide animation — PowerPoint Morph transitions, Keynote-style continuous motion, shapes that grow / move / rotate as the slide advances. Trigger on: 'morph', 'morph transition', 'smooth transition', 'continuous animation across slides', 'Keynote-style transition', 'animated slide sequence', 'shape continuity across slides'. Output is a single .pptx. This skill is a scene layer on top of officecli-pptx — inherits every pptx v2 rule (visual floor, grid, palettes, connector canon, Delivery Gate 1–5a). DO NOT invoke for a generic deck, pitch deck, or board review without cross-slide motion — route those to officecli-pptx base or officecli-pitch-deck.

stanfish06 Bundle

Reviews a reverse-skill case package for scope readiness, Evidence to Finding to Path traceability, work item coverage, timeline references, and optional artifact hash integrity before report handoff.

stanfish06 Bundle

Use when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.

stanfish06 Bundle

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

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Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.

stanfish06 Bundle

Annotate VCF variants with Ensembl VEP, ClinVar, and gnomAD. Ranks variants by impact (HIGH/MODERATE/LOW/MODIFIER) and generates a reproducible report.

stanfish06 Bundle

Use when asking about Rust versions or crate info. Keywords: latest version, what's new, changelog, Rust 1.x, Rust release, stable, nightly, crate info, crates.io, lib.rs, docs.rs, API documentation, crate features, dependencies, which crate, what version, Rust edition, edition 2021, edition 2024, cargo add, cargo update, 最新版本, 版本号, 稳定版, 最新, 哪个版本, crate 信息, 文档, 依赖, Rust 版本, 新特性, 有什么特性

stanfish06 Bundle

Cell segmentation in fluorescence microscopy images. Supports Cellpose/cpsam (Cellpose 4.0) with additional backends planned. Produces segmentation masks, per-cell morphology metrics (area, diameter, centroid, eccentricity), overlay figures, and a report.md.

stanfish06 Bundle

Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build a citation graph — all locally, with a reproducibility bundle.

stanfish06 Bundle

Personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevant SNPs and generates actionable dietary guidance, all computed locally.

stanfish06 Bundle

Build a complete Nature-style Chinese PPTX presentation from a scientific paper, preprint, PDF, article text, figure legends, or reading notes. Use for journal club, group meeting, thesis seminar, paper sharing, conference or defense decks, and Chinese requests such as 论文做PPT、论文汇报、组会PPT、文献汇报、学术汇报、做幻灯片、读书报告PPT. It classifies paper type, builds an evidence-led story, selects key figures, writes Chinese slide content and speaker notes, creates the actual .pptx, and runs corrective QA for complete figure crops, stable alignment, text overflow, and de-templated Chinese academic expression. Also trigger when improving weak paper-to-PPT output with cropped figures, loose alignment, obvious AI-style wording, or heavy manual rework.

stanfish06 Bundle

Gene-set pathway enrichment analysis using Enrichr — queries KEGG, GO (BP/MF/CC), Reactome, WikiPathways, MSigDB, and Disease Ontology. Produces ranked pathway tables, interactive bubble charts, and a reproducible Markdown report.

stanfish06 Bundle

Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs

stanfish06 Bundle

Publication-quality PDF report generation using Typst templates. Produces professional scientific reports with colored section bands, styled tables, figure captions, callout boxes, and page headers/footers.

stanfish06 Bundle

Protein structure prediction with Boltz-2. Accepts YAML inputs (single protein or multi-chain complex), runs boltz predict, extracts per-residue pLDDT and PAE confidence, and writes a markdown report with figures.

stanfish06 Skill

Use this skill any time a .docx file is involved -- as input, output, or both. This includes: creating Word documents, reports, letters, memos, or proposals; reading, parsing, or extracting text from any .docx file; editing, modifying, or updating existing documents; working with templates, tracked changes, comments, headers/footers, or tables of contents. Trigger whenever the user mentions 'Word doc', 'document', 'report', 'letter', 'memo', or references a .docx filename.

stanfish06 Skill

Use this skill any time a .pptx file is involved -- as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx file; editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates, layouts, speaker notes, or comments. Trigger whenever the user mentions 'deck', 'slides', 'presentation', 'pitch', or references a .pptx filename.

stanfish06 Bundle

Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.

stanfish06 Bundle

Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.

stanfish06 Bundle

Generate a presentation package from a finalized bio-manuscript proposal. Use when producing a 10-15 slide, Markdown-first presentation outline (group-meeting / 组会 style) from FINAL_PROPOSAL.md plus demo or validation results.

stanfish06 Bundle

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). Use when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

stanfish06 Bundle

Generate or improve MATLAB help text (documentation comments) for a function, class, or script file following MathWorks standards (H1 line, syntax paragraphs, See Also, 75-char lines). Read BEFORE writing MATLAB help — default patterns (Inputs:/Outputs: lists, block comments, uppercase See Also) produce non-conforming output. Use when writing, rewriting, fixing, or reviewing MATLAB help comments or function documentation.

stanfish06 Bundle

Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.

stanfish06 Skill

Use this skill when the user is building a fundraising / investor pitch deck — seed, Series A / B / C, convertible note, SAFE round, strategic raise. Trigger on: 'pitch deck', 'investor deck', 'Series A deck', 'Series B deck', 'Series C deck', 'fundraising deck', 'seed pitch', 'VC deck', 'raising capital', 'term sheet presentation'. Output is a single .pptx. This skill is a scene layer on top of officecli-pptx — inherits every pptx v2 rule (visual floor, grid, palettes, connector canon, Delivery Gate). DO NOT invoke for a generic board review, sales deck, all-hands, or product launch — route those to officecli-pptx base.

stanfish06 Bundle

Internal maintenance support for checking and fixing generated Rust skill documentation references. Use only when explicitly invoked by /fix-skill-docs.

stanfish06 Skill

Use this skill to create fillable Word forms (.docx) with real Content Controls (SDT) + legacy FormField checkboxes + MERGEFIELD mail-merge placeholders + document protection. Trigger on: 'fillable form', 'form fields', 'content controls', 'SDT', 'word form', 'fill in', 'only editable fields', 'protect document', 'onboarding form', 'HR intake', 'survey template', 'contract / SOW template', 'mail-merge template', 'compliance checklist', 'medical intake questionnaire'. Output is a single .docx where specific fields are editable and the rest is locked. This skill is INDEPENDENT, not a scene layer on docx — payload is `<w:sdt>` + `<w:ffData>` + `<w:fldChar>` + `documentProtection`, none of which docx base skill covers. Do NOT trigger for regular reports, letters, memos, academic papers, pitch decks, or any document with no user-fillable fields — route those to officecli-docx or its scene layers.

stanfish06 Skill

Spatial omics workflows with SpatialData and Squidpy alongside scanpy, anndata, and napari-viz. Use when working with Visium, Xenium, CosMx, MERFISH, Slide-seq, spatial transcriptomics, spatial proteomics, tissue images linked to AnnData, spatial neighbor graphs, spatial autocorrelation, ligand-receptor proximity, image features, or napari-spatialdata.

stanfish06 Bundle

Use at the start of computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.

stanfish06 Bundle

Generates all documentation artifacts for a MATLAB toolbox: README.md, functionSignatures.json, GettingStarted.m, and publishable examples with demos.xml help integration. Follows mathworks/toolboxdesign best practices. Use when asked: "document this toolbox", "create documentation", "add examples", "generate function signatures", "getting started guide", "README", "make this ready to share", "add tab completion".

stanfish06 Bundle

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. Use when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.

stanfish06 Bundle

Guides the 7-step MATLAB memory optimization workflow: baseline, profile, identify, optimize, measure, verify, report. Use when asked to reduce MATLAB memory usage, find memory bottlenecks, fix out-of-memory errors, or optimize memory-intensive code.

stanfish06 Bundle

Create, edit, and run plain-text MATLAB live scripts (.m files) with rich text formatting, LaTeX equations, section breaks, and inline figures. Use when generating tutorials, analysis notebooks, reports, documentation, or educational content, when modifying existing live scripts, or when converting existing binary .mlx files to .m for version control. Requires R2025a+.

stanfish06 Bundle

Generates professional clinical PDF reports in English from WES (Whole Exome Sequencing) data with clinical interpretation summary, pharmacogenomic alerts, and follow-up recommendations.

stanfish06 Bundle

Generates professional clinical PDF reports in Spanish from WES (Whole Exome Sequencing) data with clinical interpretation, pharmacogenomic alerts, and follow-up recommendations.