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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.

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 No longer maintained.

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.

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.

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.

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.

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 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.

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.

Google's official skills for building ADK agents: dev workflow, scaffolding, the ADK Python API, evaluation with LLM judges and adaptive rubrics, deployment to Agent Runtime, Cloud Run or GKE, publishing and observability. Works with agents-cli; local dev needs only an AI Studio key.

250+ MCP tools for Ghidra: decompilation, cross-references, data-flow analysis, bulk renaming and commenting, P-code emulation and live debugging, with headless mode support. Requires Java 21 and Ghidra 12.1, and the plugin must be built and deployed first.

Posit's open-source scientific and technical publishing system built on Pandoc: embed Python, R or Julia code in Markdown or Jupyter notebooks, then quarto render produces HTML, PDF, Word, slides, websites and books.

Semi-automated research assistant for CS and AI researchers that links ideation, Zotero literature management, experiment analysis and reporting, paper writing and reviewer responses, and keeps project knowledge in Obsidian. Branches for Codex and other agents exist.

Semi-automated research workflow for computer science and AI researchers: ideation, Zotero literature management, experiment analysis and reports, paper writing and polishing, and rebuttals, with optional Obsidian knowledge base. 40+ skills; also installable as a Claude Code plugin.

From the FinanceToolkit author: computes ratios, valuation, risk and macro indicators with 500+ transparent formulas, for company comparisons and first-pass due diligence. Hosted, no install; enter a Financial Modeling Prep key on first connect (free tier: US stocks, 5 years). Verify results.

Detects shot changes in video and splits long footage into scenes, exporting cut lists and per-scene thumbnails, useful for shot analysis, organizing footage and finding edit points. Runs locally; needs Python 3.10+, plus FFmpeg or mkvmerge for splitting.

LM Studio's official CLI: list, load and unload local models, start and stop the local API server, and check status and logs; ls, ps and other commands support --json output for scripts and agents. Requires the LM Studio desktop app.

Lingo.dev's official CLI: lingo push sends JSON, YAML, Markdown, PO, XLIFF, Android/Xcode strings and other files from your repo to its LLM localization engine, and lingo pull brings translations back; CI-ready. Needs a Lingo.dev account; usage-based pricing with a free sandbox.

Classic CLI for reading and writing metadata in hundreds of file types including images, video, audio and PDF, covering EXIF, GPS, IPTC, XMP and camera makers' proprietary tags, with batch editing, stripping and conversion. Requires Perl.

CLI and TypeScript runtime for discovering and calling MCP servers from the terminal and scripts: list tool signatures and call tools directly, or generate a standalone CLI or typed client from a server. Auto-imports existing MCP configs from Claude Code, Codex and others.

Empirical social science skills from Stanford REAP and CoPaper.AI, bundling 77 in-house and third-party collections: topic selection, literature reviews, DID/RD/IV identification, regression tables in Python, Stata or R, robustness audits and paper writing. Stata flows need Stata installed.

Draws bar charts, histograms, line charts, scatter plots and box plots in the terminal from CSV/TSV on stdin, so you can glance at data distributions at the end of a shell pipeline. The command is uplot.