Docs & Writing

bookforge-ai Bundle

Evaluate object-oriented designs against the two foundational GoF principles: 'Program to an interface, not an implementation' and 'Favor object composition over class inheritance.' Use when reviewing class hierarchies, assessing reuse strategies, or deciding between inheritance and composition for a specific design problem. Identifies violations like white-box reuse, broken encapsulation from subclassing, concrete class coupling, delegation overuse, and inheritance hierarchies that should be flattened. Use when someone says 'should I use inheritance or composition here', 'is this class hierarchy right', 'my subclass is breaking when the parent changes', 'how do I make this more flexible', 'is this design too rigid', 'I want to change behavior at runtime', or 'review my OO design for best practices'. Produces a design principle compliance report with specific violations and recommended refactoring.

bookforge-ai Skill

Optimize code performance by first refactoring to a well-factored structure, then running a profiler to find actual hot spots, and applying targeted optimizations only where the profiler points — never by guessing. Use this skill when users report the program is too slow, before any performance work begins on an unfactored codebase, or after refactoring is complete and performance must now be tuned to acceptable levels.

oimiragieo Bundle

Parses and merges Claude .jsonl transcripts with debug logs to generate a timeline heuristics report of API limits, context overflows, hook blocks, and tool failures.

oimiragieo Bundle

Master network protocol reverse engineering including packet analysis, protocol dissection, and custom protocol documentation. Use when analyzing network traffic, understanding proprietary protocols, or debugging network communication.

aradotso-trending-skills Skill

Native macOS Markdown viewer app with Quick Look extension, Mermaid diagrams, KaTeX math, document outline, and editor integration

duc01226 Skill

[Testing] Use when reviewing a running user experience or observable output (UI, API, CLI, service) — run it locally, drive it end to end like a user, gate on runtime/console logs and captured screens, set a baseline, or adjudicate a regression. Flag: --rounds=N (default 3; 0 = report-only).

aradotso-trending-skills Skill

Conversation-first, image-first PPT generation workflow skill using GPT Image 2 for full-page visual slides packaged into PPTX files.

aradotso-trending-skills Skill

KillerPDF is a portable, single-EXE Windows PDF editor built with C#/WPF and PDFium — supports viewing, annotating, merging, splitting, signing, and printing PDFs with no installer, account, or telemetry.

g1joshi Skill

Obsidian knowledge management with markdown. Use for note-taking.

aradotso-trending-skills Skill

Work with Keychron's source-available CAD hardware design files (STEP/DXF/PDF) for keyboards and mice, including scripting, inventory management, and 3D printing workflows.

oimiragieo Bundle

PowerPoint presentation generation using python-pptx. Create slides from Claude output, data analysis, or structured content. Covers slide templates, shapes, charts, tables, and themed presentations. Use for generating .pptx files programmatically.

gptomics Bundle

Maps cell-cell communication and ligand-receptor co-expression in spatial transcriptomics (Visium, Xenium, MERFISH, CosMx, Slide-seq) with Squidpy ligrec, COMMOT, stLearn, CellChat-spatial, and NicheNet. Use when choosing a method by whether spatial distance is actually modeled (squidpy ligrec is space-blind cluster-permutation vs COMMOT optimal-transport is distance-aware vs stLearn neighborhood vs CellChat-spatial filter) and by secreted-vs-contact-dependent range; choosing the ligand-receptor database knowingly because it drives the result as much as the algorithm; guarding against segmentation-spillover circularity that fabricates short-range hits; treating every ligand-receptor score as a co-expression hypothesis on a confidence ladder, not validated signaling; correcting for thousands of pair-by-cell-type-pair permutation tests; and recognizing that a targeted imaging panel rarely contains the relevant ligands and receptors so a "no communication" call is uninformative.

gptomics Bundle

Estimates per-spot cell type composition of spatial transcriptomics mixtures (Visium, Slide-seq, Stereo-seq) from an scRNA-seq reference with cell2location, RCTD, SPOTlight, stereoscope, SpatialDWLS, or reference-free STdeconvolve. Use when deciding whether a platform even needs deconvolution (the resolution fork -- a 55um Visium spot is a 1-10-cell MIXTURE -> deconvolve, but a Xenium/MERFISH/CosMx cell is already single -> segment instead, and running deconvolution there invents fractions that do not exist); choosing cell2location (absolute abundance) vs RCTD/SPOTlight/stereoscope/SpatialDWLS (proportions only) by output and runtime; matching the scRNA reference to tissue and condition (the reference IS the result -- a missing cell type is silently misassigned to its nearest neighbor with no error flag); and handling compositional outputs that sum to 1 with CLR/ILR rather than naive per-type t-tests.

gptomics Bundle

Plots spatial transcriptomics expression, clusters, and annotations on tissue using Squidpy and Scanpy. Use when choosing the plotter and spot size by platform fork (sc.pl.spatial / sq.pl.spatial_scatter with real scalefactors and capture diameter for spot/capture data like Visium and Slide-seq, versus molecule/segmentation overlays for imaging/FOV data like Xenium, MERFISH, and CosMx); getting the histology coordinate-frame transform right (micron<->pixel, scalefactors) so points land on the image; and avoiding the honest-visualization traps where interpolation/KDE manufactures spatial pattern not in the data, oversized markers fake tissue coverage, jet and other non-uniform colormaps distort structure, and non-metric UMAP/tSNE distances are misread as spatial conclusions.

oimiragieo Bundle

Use when creating, updating, or generating README and documentation files for projects and libraries

oimiragieo Bundle

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

gptomics Bundle

Reconstructs single cells from sub-cellular spatial capture units (Visium HD 2um bins, Stereo-seq DNB spots, Slide-seqV2 beads) by aggregating bins UP into cells rather than deconvolving a mixture DOWN. Use when choosing a bin size and recognizing the sparsity-vs-mixture dilemma (2um bins are too sparse to cluster, but binning to 8/16um re-creates the multi-cell mixture deconvolution was meant to escape); deciding between morphology-driven cell reconstruction (Bin2cell -- StarDist/Cellpose nuclei on a registered H&E/DAPI image, then assign 2um bins to nuclei) and fixed-bin aggregation by whether a co-registered cell image exists; recognizing this as the INVERSE of deconvolution (bin UP, not mix DOWN -- this is the AMBIGUOUS regime of the resolution fork); and handling each platform (Visium HD has an image so reconstruct, Slide-seqV2 has no per-bead image so aggregate or deconvolve, Stereo-seq depends on a registered stain).

oimiragieo Bundle

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.

oimiragieo Bundle

This skill should be used 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.

g1joshi Skill

Confluence team documentation platform. Use for documentation.

oimiragieo Bundle

Verify completed work against acceptance criteria, collect evidence, and produce a PASS/FAIL UAT report

oimiragieo 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.

ariffazil Bundle

This skill should be used when the user needs to analyze Git repositories, compare developer commit patterns, work habits, development efficiency, code style, code quality, and slacking behaviors. It generates honest, direct developer evaluations with scores, grades, strengths, weaknesses, and actionable suggestions. Trigger phrases include "analyze code", "analyze repository", "compare developers", "code quality report", "commit patterns", "developer efficiency", "developer evaluation", "slacking index", "摸鱼指数", "工作习惯分析", "代码分析", "研发效率", "代码质量", "开发者评估", "developer score".

oimiragieo Bundle

Creates rule files for the Claude Code framework. Rules are markdown files in .claude/rules/ that are auto-loaded by Claude Code.

ariffazil Bundle

Translate internal federation and epistemic vocabulary into publication-grade geological prose before rendering human-facing PDF artifacts.

oimiragieo Bundle

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used 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.).

oimiragieo Bundle

Generates comprehensive documentation from code, APIs, and specifications. Creates API documentation, developer guides, architecture docs, and user manuals with examples and tutorials.

oimiragieo 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.

oimiragieo Bundle

PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.

oimiragieo Bundle

Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.

ariffazil Bundle

VSS-2 Lightweight Verifier Suite — independent post-generation verifiers for Verified Scene Synthesis. Wraps vision_analyze with three focused checks (Count/Containment, Perspective/Depth, Shadow/Light Direction) producing structured Hard/Soft Violation reports. Pure OBSERVATION — never mutates, never judges. 555-ASI gates output before reasoning. USE WHEN: "verify this generated image", "check if generation has violations", "run VSS verifiers", "post-generation QA", "Hard/Soft Violation report".

oimiragieo Bundle

This skill should be used at the start of any 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.

oimiragieo Bundle

Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.

oimiragieo Bundle

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used 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.

oimiragieo Bundle

TDD applied to documentation - create production-ready skills. Use when authoring new skills. Includes writing style guidelines for clear prose.

ariffazil Bundle

OCR as optical context compression. Converts documents/images to structured markdown using a VLM cascade (qwen3-omni-flash → Tesseract → RapidOCR). Use when processing scanned documents, tables, charts, or images containing text. Includes F2/F4/F9/F12 constitutional gates. Trigger phrases include "OCR", "extract text from image", "document to markdown", "parse table from image", "scan document".