Tools

Open-source research agent: one command runs literature reviews, deep research, paper reviews, paper-code consistency checks and replication plans, searching arXiv, PubMed and more with sources recorded. Good for grad students writing reviews. Run feynman setup to sign in to a model provider.

Processes CSV, TSV, JSON and other structured data like awk, sed, cut, join and sort, but by field name, for cleaning, aggregation, format conversion and pretty-printing. The command is mlr; written in Go with no runtime dependencies.

Linter and formatter for 20+ SQL dialects that auto-fixes most issues and handles Jinja templating and dbt projects (dbt needs a plugin), suited to warehouse code review and CI.

Extracts the main content of a web page, stripping comments, sidebars, headers and footers, and outputs clean HTML or Markdown with metadata like title, author and publish date, saving tokens when agents read the web. Built for Obsidian Web Clipper by kepano; still in development.

NVIDIA's open-source LLM vulnerability scanner that probes for prompt injection, jailbreaks, data leakage, hallucination and harmful content, supporting OpenAI, Hugging Face, Bedrock and most REST-accessible models. Scanning cloud models needs their API keys.

Official AWS MCP for managing FHIR health data in AWS HealthLake: CRUD, advanced search, full patient records, and import and export, with a read-only mode to prevent changes. Needs an AWS account, a paid HealthLake data store and local AWS credentials; clinical conclusions need professional review.

PDF translation CLI for research papers that preserves formulas and layout as much as possible, producing bilingual side-by-side or translation-only PDFs. Needs an OpenAI-compatible API (local Ollama works too); currently focused on English to Chinese.

Distributed data integration tool and Apache top-level project with 160+ connectors for batch, real-time and CDC sync. Define jobs in config files and run them on the built-in Zeta engine or on Flink or Spark. Requires Java.

High-accuracy retrieval-augmented Q&A over paper PDFs, text and Office documents, filling in citation metadata, checking retractions and attaching traceable sources to answers. Provides the pqa CLI and a Python library. Needs an LLM API key by default; local models can be configured.

Deep research assistant that runs locally with a built-in MCP server: searches arXiv, PubMed, Wikipedia and more over multiple rounds and writes cited reports. Needs Python 3.12+, uv and an LLM (local Ollama or an API key); web search needs SearXNG or similar. Runs take minutes to half an hour.

Terminal tool for exploring and wrangling tabular data: opens dozens of formats including CSV, JSON, Excel and SQLite for filtering, sorting, pivots and frequency counts. --batch mode replays actions headlessly or converts file formats.

Say build a harness for this project and it designs a domain-specific agent team, generating subagent definitions, companion skills and orchestration, validates them and keeps evolving them from feedback. Supports workflow orchestration, persistent agent teams and subagent delegation.

Manage database schemas as code: declare the desired schema in SQL, HCL or your ORM and Atlas plans, lints and applies migrations, and can export existing databases as HCL, SQL or Mermaid ER diagrams. Supports PostgreSQL, MySQL and a dozen other databases.

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.

Google Workspace CLI for scripts and agents covering Gmail, Calendar, Drive, Docs, Sheets, Contacts and Tasks, with JSON output, read-only mode and command allowlists; can also run as a read-only-by-default MCP server. Bring your own Google OAuth client.

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.

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.

Removes backgrounds from images and videos with one AI command: batch whole folders, use a portrait model, refine edges or swap in a solid color, and output transparent MOV or composite video onto a new background. Runs locally; install PyTorch and ffmpeg first. Models download on first run.

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.

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.

Cuts long videos like podcasts, webinars, livestreams and interviews into captioned vertical shorts, with optional dubbing and publishing to TikTok, YouTube and more. Hosted version needs an API key (free tier is watermarked and time-limited), or self-host with Docker and your own keys.

ClickUp's official plugin in OpenAI's Codex marketplace: search your whole ClickUp workspace in natural language, find, create, update and manage tasks, and check whether a project or sprint is at risk of slipping. Codex only; needs a ClickUp account and authorization.

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.

Higgsfield's official Codex plugin: uses its remote MCP to generate images and video from text or photos, like product-shot video ads or animated stills, with built-in flows for faceless narration, voiceover and burned-in captions. Needs a Higgsfield account; billed in credits.