Tools

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 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.

From Trail of Bits: starts from one confirmed vulnerability, distills its root cause, then writes and progressively generalizes CodeQL/Semgrep queries to find similar variants across the codebase and report them by severity.

From Trail of Bits: reviews PRs, commits or diffs from a security angle, tracing history with git blame, estimating blast radius by caller count and checking test coverage gaps, then writes a Markdown review report.

Plugin marketplace from security firm Trail of Bits with 40+ plugins for code auditing, CodeQL/Semgrep static analysis, variant analysis, supply-chain risk, smart contract security and reverse engineering. Codex can load it directly too.

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.

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.

Anthropic's reference implementation for finding and fixing vulnerabilities: Claude Code skills for threat modeling, static scanning, triage and patching, plus an autonomous recon-to-patch pipeline (C/C++ memory bugs by default; needs Docker and gVisor). No longer maintained.

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.

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 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.

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 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 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.

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.

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.

Security scans for a whole repo or for changes like PRs and commits, with threat modeling, vulnerability triage, fixes and re-verification; reports export to JSON, SARIF and more. OpenAI's official Codex plugin; requires Codex Security access.

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.

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.

Converts and two-way syncs Jupyter notebooks with plain Python scripts or Markdown, so agents can edit research and teaching notebooks like ordinary text and diffs stay readable. Needs a local Python environment; install with pip.

Cleans a LaTeX project before arXiv submission: removes comments, auxiliary files and unused .tex files and images, and can compress images, so internal notes are not published with the source. From Google Research; installable with Homebrew on macOS.

Python library and CLI for extracting main web content: fetches pages, crawls via sitemaps and RSS feeds, strips headers, footers and other noise, and outputs TXT, Markdown, JSON, XML and more with metadata. Also processes downloaded HTML offline.