Tools

Publication-quality matplotlib plotting skill from a Yale PhD student: bar charts, trends, heatmaps and multi-panel figures with consistent fonts, colors and export settings, plus real plotting scripts from papers published in venues like Nature Machine Intelligence. Needs Python.

Converts the output of 100+ commands such as dig, ps, ls and ifconfig, plus common file formats, into JSON so agents can parse it reliably with jq or scripts. Also usable as a Python library.

Open-source visual traceroute that shows IP geolocation, AS number and carrier for every hop, with continuous MTR probing and JSON output; the full edition can also be deployed as an MCP server.

Offline speech toolkit for Apple Silicon Macs: CLI text-to-speech (including Chinese and voice cloning) and speech-to-text, for voicing lessons and explainer videos or transcribing lectures and interviews, with data staying local. Needs an M-series Mac and Python 3.10+; MP3 export needs ffmpeg.

Query, modify and convert JSON, YAML, TOML, XML, CSV, HCL, INI and more with one selector syntax, editing config files in place or converting between formats, handy for agents handling structured data in scripts. A single dependency-free binary that works much like jq or yq.

Query cloud resources and SaaS APIs live with SQL: plugins map AWS, Azure, GCP, GitHub, Kubernetes and other services to tables you can select from directly, no ETL needed. A single binary with Postgres built in.

asc CLI for scripting the App Store Connect API: manage builds, TestFlight, metadata, signing and review submissions to automate iOS and macOS releases from the terminal or CI. Ships with a companion agent skill pack. Needs an App Store Connect API key.

Diffusion model inference in pure C/C++: one sd-cli command runs SD, FLUX, Qwen Image, Wan and more locally to create or edit images and short videos, with Metal acceleration on Mac. No cloud needed; bring your own model weights and use a release binary or build from source.

Trail of Bits skill that audits GitHub Actions workflows wired to AI coding agents (Claude Code Action, Codex, Gemini CLI and others) for prompt injection, env-variable relays, dangerous sandbox settings, wildcard allowlists and other privilege risks.

Trail of Bits skill that audits npm, PyPI and Go supply-chain risk: known advisories across direct deps and the whole lockfile tree, deprecated or archived upstreams, npm publisher concentration and install-time scripts. Needs uv; a logged-in gh is recommended.

Trail of Bits static analysis skills: CodeQL for interprocedural taint tracking and data-flow analysis, Semgrep for rule-based scanning, plus parsing and deduplicating SARIF results. Requires CodeQL or Semgrep installed locally.

Turns Peng Sida's public research-writing notes into a skill: revises abstracts, introductions, methods and experiments of ML/CV/NLP papers from a reviewer's view, checks that each claim has experimental evidence, and runs a pre-submission self-check. Pure methodology, no API key.

Manage Kubernetes clusters in natural language: translates intent into kubectl operations and runs them, and can serve as an MCP server for other agents. Uses Gemini by default (API key required) and also supports OpenAI and local models. Maintained by Google Cloud.

Open-source LLM evaluation platform: one opencompass command picks the model and datasets and runs the evaluation across hundreds of benchmarks. Works with local Hugging Face models and API models, with vLLM and LMDeploy for faster inference.

OpenAI's official life-science skills: 49 skills query public databases such as UniProt, ClinVar, gnomAD and AlphaFold through Python scripts, with a router skill that breaks down questions, normalizes entities and compiles sourced evidence. Written mainly for Codex.

OpenAI's official data analytics skills: data quality assessment, KPI design, metric anomaly diagnosis, dashboards and analysis reports, market sizing and notebooks. Ships with a Codex plugin; some skills depend on its runtime.

Creates, edits and validates reproducible Python and SQL Jupyter notebooks: organizes cells as reports or tutorials, checks conclusions against actual output and reruns top to bottom before handoff. Maintained by OpenAI in the Data Analytics plugin of openai/plugins.

OpenAI's official Codex plugin that guides sequencing analysis from BCL/FASTQ: QC, RNA-seq differential expression, single-cell, variant calling and metagenomics, favoring nf-core and other public pipelines with reproducible run logs. Checks for local tools first. Research use only.

OpenAI's official Codex plugin with 18 skills to choose, design, build, test and export web charts, maps, dashboards, Gantt charts and UML, using D3, Vega-Lite and Three.js with attention to accessibility and responsiveness. Codex only.

Build with OpenAI best practices inside Codex: call the OpenAI API, build and deploy agents with the Agents SDK, create ChatGPT apps and prepare submission materials, and create API keys directly. Maintained by OpenAI; Codex only.

OpenAI's official Codex plugin with about 50 skills that route questions to genetics, omics, pathway, protein structure, chemistry and clinical evidence sources, can split the work across parallel subagents, and synthesize sourced conclusions.

OpenAI's official Codex plugin for answering product and business questions with data: metric anomaly diagnosis, KPI design, market sizing, dashboards and reports, notebooks and data quality checks. Connects to data warehouses and BI tools.

OpenAI's official set of 18 web data visualization skills: chart selection and critique, D3, Canvas, Three.js, maps, statistical uncertainty, live dashboards, Gantt charts, UML and scrollytelling. Ships with a Codex plugin; installed alone, the plugin-level references are missing.

A more intuitive find-and-replace tool than sed: uses JavaScript/Python-style regex syntax, supports literal string mode and in-place file edits, which suits agents doing bulk text rewrites.