CLI Tools
Command line utilities
fluidsim
by K-Dense-AI
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
generate-image
by K-Dense-AI
Generate or edit images using AI models (FLUX, Gemini). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.
arboreto
by K-Dense-AI
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
gtars
by K-Dense-AI
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
gget
by K-Dense-AI
"Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices."
diffdock
by K-Dense-AI
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
pup
by datadog-labs
Datadog API CLI with 49 command groups, 300+ subcommands. Skills and domain agents for monitoring, logs, APM, security, and infrastructure.
git-guardrails-claude-code
by mattpocock
Set up Claude Code hooks to block dangerous git commands (push, reset --hard, clean, branch -D, etc.) before they execute. Use when user wants to prevent destructive git operations, add git safety hooks, or block git push/reset in Claude Code.
humanize-chinese
by brycewang-stanford
Detect and humanize AI-generated Chinese text. 20+ rule detection categories plus statistical features (sentence-length CV, short-sentence fraction, comma density, perplexity, GLTR, DivEye) plus scene-aware LR fusion (rule × 0.2 + LR × 0.8) trained on three scenes: general / academic / longform 长文本 (≥1500 字)。Unified CLI: ./humanize {detect,rewrite,academic,style,compare}. 8 style transforms (casual/zhihu/xiaohongshu/wechat/academic/literary/weibo/novel)。 Multi-paragraph rewriting (paragraph length CV、跨段 trigram 重复) plus best-of-N humanize (默认 N=10 取最低 LR)。165 replacement patterns + CiLin 同义词词林 38873 with collision blacklist。 Academic paper AIGC reduction for CNKI/VIP/Wanfang (知网/维普/万方 AIGC 检测降重)。 Pure Python, no dependencies, offline。v5.0.0 — HC3 fused 准确率 95%、学术 hero 100→35 (-65)、 工作汇报 96→13 (-83)、长篇博客 96→41 (-55)。 Use when user says: "去AI味", "降AIGC", "人性化文本", "humanize chinese", "AI检测", "AIGC降重", "去除AI痕迹", "文本改写", "论文降重", "知网检测", "维普检测", "AI写作检测", "让文字更自然", "detect AI text", "humanize text", "reduce AIGC score", "make text human-like", "去ai化", "改成人话", "去机器味", "降低AI率", "过AIGC检测", "长文本改写", "小说改写"
openalex
by brycewang-stanford
Use when the user asks about academic literature, research papers, scholarly works, authors, citations, institutions, journals, or any academic metadata. Trigger when users want to search for papers, find author profiles, track citations, discover related works, or explore academic topics. Also use when users mention DOIs, ORCIDs, h-index, publication venues, or research metrics.
marp-export
by brycewang-stanford
Export Marp slide markdown files to PDF (default), HTML, PPTX, or PNG. Handles theme loading, Chrome/Chromium detection for PDF export, and batch conversion. Trigger when user says "export slides", "convert marp to pdf", "marp export", "slides to pdf", "slides to html", "导出slides", "slides转pdf", "导出演示文稿".
bisect-aware-instrumentation
by ArabelaTso
Instrument code to support efficient git bisect by producing deterministic pass/fail signals and concise runtime summaries for each tested commit. Use when debugging regressions with git bisect, automating bisect workflows, creating bisect test scripts, handling flaky tests during bisection, or needing clear exit codes and logging for automated bisect runs. Helps identify the exact commit that introduced a bug through automated testing.
agent-browser
by ArabelaTso
CLI-based browser automation with persistent page state using ref-based element interaction. Use when users ask to navigate websites, interact with web pages, fill forms, take screenshots, test web applications, or extract information from web pages.
mcp:setup-codemap-cli
by NeoLabHQ
Guide for setup Codemap CLI for intelligent codebase visualization and navigation
customaize-agent:create-hook
by NeoLabHQ
Create and configure git hooks with intelligent project analysis, suggestions, and automated testing
git:compare-worktrees
by NeoLabHQ
Compare files and directories between git worktrees or worktree and current branch
git:merge-worktree
by NeoLabHQ
Merge changes from worktrees into current branch with selective file checkout, cherry-picking, interactive patch selection, or manual merge
git:create-worktree
by NeoLabHQ
Create and setup git worktrees for parallel development with automatic dependency installation
customaize-agent:create-command
by NeoLabHQ
Interactive assistant for creating new Claude commands with proper structure, patterns, and MCP tool integration
git:notes
by NeoLabHQ
Use when adding metadata to commits without changing history, tracking review status, test results, code quality annotations, or supplementing commit messages post-hoc - provides git notes commands and patterns for attaching non-invasive metadata to Git objects.
mcporter
by NousResearch
Use the mcporter CLI to list, configure, auth, and call MCP servers/tools directly (HTTP or stdio), including ad-hoc servers, config edits, and CLI/type generation.
llava
by NousResearch
Large Language and Vision Assistant. Enables visual instruction tuning and image-based conversations. Combines CLIP vision encoder with Vicuna/LLaMA language models. Supports multi-turn image chat, visual question answering, and instruction following. Use for vision-language chatbots or image understanding tasks. Best for conversational image analysis.
gguf-quantization
by NousResearch
GGUF format and llama.cpp quantization for efficient CPU/GPU inference. Use when deploying models on consumer hardware, Apple Silicon, or when needing flexible quantization from 2-8 bit without GPU requirements.
imessage
by NousResearch
Send and receive iMessages/SMS via the imsg CLI on macOS.