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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 that makes Google Drive the single entry point to search, organize, share and export files, handing Docs, Sheets, Slides and comments to dedicated sub-skills for summaries, edits and new files. Authorize your Google account in Codex.

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.

Notion's plugin in OpenAI's official Codex marketplace: uses the Notion connector and hosted MCP to search and update workspace pages, with skills for spec-to-implementation plans, research write-ups, meeting prep and knowledge capture. Codex only; needs Notion authorization.

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 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.

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 No longer maintained.

Command-line email client supporting IMAP, SMTP, JMAP, Gmail and Microsoft Graph, with multiple accounts and --json output, so agents can check, search, compose and send mail. A first-run wizard auto-detects your mailbox settings.

Claude Code workspace for long-form SEO blogging: /research, /write, /rewrite and /optimize handle keyword research, drafting, refreshes and pre-publish checks, with SEO, metadata and internal-link subagents. Clone the repo and add brand voice; optional GA4, Search Console and WordPress.

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.

Tw93's lean pack of engineering-habit skills: /think to pressure-test plans, /hunt for root causes, /check to review diffs, /ui for frontend interfaces, /write to polish Chinese and English prose, and more (8 skills). Works with both Claude Code and Codex.

Turns a theme, a line, an article or photos into a minimal, whitespace-heavy indie-zine portrait poster, and can distill reusable style rules and prompts from reference images, with built-in quality checks. Needs host image generation (e.g. Codex); otherwise outputs prompts only.

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.

Anthropic's official OS-level sandbox CLI: restricts file and network access for agents, MCP servers and any command without containers, using sandbox-exec on macOS and bubblewrap on Linux. Currently a research preview.

Static security analysis for CI/CD config: finds template injection, credential leaks, excessive permissions and more in GitHub Actions workflows, also covers Dependabot and pre-commit configs, and auto-fixes some findings.

Generates template-driven charts as single-file HTML: picks a chart from real Lupi, Basics, Glance, Maps and Interactive gallery implementations based on data shape, or fills one of 12 Chinese and English report templates. Defaults to Mono grayscale with semantic color presets. Written in Chinese.

Open-source alternative to NotebookLM's podcast feature: turns web pages, PDFs, images, YouTube videos or text into two-host conversational audio, useful for lecture notes or articles. Uses Gemini and OpenAI API keys by default, or local models plus free Edge TTS.

One command extracts or summarizes web pages, PDFs, YouTube videos, podcasts and media files, with JSON output. Summaries can use many model APIs, local models or a logged-in Codex or Claude CLI; plain extraction needs no key. Also has a browser sidebar extension.

Open-source offline machine translation built on OpenNMT, usable as a CLI, Python library or GUI. Download language packages as needed; when no direct model exists it pivots through an intermediate language. Suits text you would rather not upload to the cloud.

Unofficial nlm CLI and MCP server for NotebookLM (now Gemini Notebook): bulk-create notebooks, import web pages and docs, and generate audio overviews, quizzes, flashcards, mind maps and slides for teaching and study. Relies on undocumented APIs and a Google sign-in, so it may break.

Unofficial CLI and MCP that let agents work with NotebookLM (now Gemini Notebook): bulk-import sources, ask questions with citations, and generate audio overviews, quizzes, flashcards, mind maps and slides. Uses undocumented APIs and may break; needs a Google sign-in and uv.

Veteran suite of CSV command-line tools: in2csv converts Excel and JSON to CSV, csvcut, csvgrep and csvsort filter and sort, csvstat computes statistics, and csvsql runs SQL directly against CSV files.