Herramientas

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.

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 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 for Outlook mail: triages your inbox, summarizes threads, extracts action items, and drafts replies or forwards, for people who handle heavy email loads. Requires Codex with a ChatGPT sign-in and an authorized Microsoft account.

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.

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.

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 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.

Turns conversations and notes into structured Notion pages such as team wikis, how-to guides, decision records and FAQs, linked to related pages. From OpenAI's official plugin repo (developer: Notion); needs the Notion MCP.

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.

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.

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.

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.