Tools

166 research skills maintained by K-Dense (formerly Claude Scientific Skills), spanning bioinformatics, cheminformatics, clinical research, materials and physics, including unified access to 78 public databases such as PubChem and UniProt. Works with Claude Code, Codex and Cursor.

Self-improving agent from Nous Research with built-in memory and a learning loop that turns experience into skills. Works with any model provider; the hermes command has a terminal UI, and a gateway connects it to Telegram, Slack and more and runs scheduled tasks.

Local MCP server built into Browser Use: lets agents navigate, click, type and extract page content, or hand multi-step tasks to the built-in browser agent. Bring your own OpenAI or Anthropic API key.

High-throughput LLM inference and serving engine: vllm serve starts an OpenAI- and Anthropic-compatible server in one command. Supports 200+ model architectures from Hugging Face, quantization and distributed inference. Aimed mainly at NVIDIA, AMD and other GPUs.

MCP server built into the adaptive Python scraping framework Scrapling: supports plain HTTP requests, browser rendering and stealth fetching, and uses CSS selectors to pass only the target content to the AI, saving tokens and filtering out prompt injection.

Adaptive web scraping framework: scrapling extract turns a page into Markdown, text or HTML in one command, with CSS selectors and browser rendering for dynamic pages, plus an MCP server (needs the ai extra). Needs Python 3.10+ and a browser install on first use.

Open-source, LLM-friendly web crawler that turns pages into clean Markdown for RAG and agents. Ships the crwl CLI and supports deep crawling and question-driven data extraction (extraction needs an LLM key). Free to self-host.

Command-line edition of the open-source OpenBB investment research platform: query stock prices, financial statements, macroeconomic and other financial data from the terminal, and automate data pulls with Routine scripts. Officially maintained; some sources need API keys.

Teaches agents standard single-cell RNA-seq analysis with Scanpy: QC, normalization, PCA/UMAP, clustering, differential expression and plots, with ready-to-run pipeline scripts and guidance on converting Seurat and other R objects to h5ad. Needs Python 3.12+; by K-Dense.

Guides agents to the right statistical method for research data: t-tests, ANOVA, chi-square, regression and Bayesian analysis, checking assumptions, computing effect sizes and power, and reporting results in APA format. Python-based (pingouin, statsmodels); by K-Dense.

Multi-language git hook manager: declare formatting, lint, secret scanning and other hooks in .pre-commit-config.yaml to run automatically before each commit, or have the agent self-check with pre-commit run --all-files before committing.

Simon Willison's LLM CLI and Python library: call OpenAI, Claude, Gemini and local models from the terminal, with conversations logged to SQLite automatically, plus embeddings, structured extraction, tool calling and a plugin system.

MySQL terminal client with smart autocompletion and syntax highlighting, also compatible with MariaDB and TiDB. Supports --execute and batch mode with CSV or table output, so agents can run SQL directly.

Bundles 60+ full-stack specialist skills into one plugin: experts for 12 languages including Python, TypeScript, Go, Rust and Java, and frameworks like React, Django and Spring Boot, activated automatically by request. Also includes Jira and Confluence workflow commands (needs Atlassian MCP).

Publishes SQLite databases as browsable, queryable web pages and JSON APIs, with SQL queries, metadata and plugins, and deploys to Cloud Run and other platforms with datasette publish. Great for data exploration and data journalism. Needs Python 3.10+.

Reads the exact position of every character, line and table cell in digital PDFs: the CLI exports layout-preserving text or CSV/JSON details, and the Python API extracts tables and form fields, ideal for invoices, statements and reports. Runs locally with Python; scans need OCR first.

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.

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.

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.

Publication-quality matplotlib plotting skill from a Yale PhD student: bar charts, trends, heatmaps and multi-panel figures with consistent fonts, colors and export settings, plus real plotting scripts from papers published in venues like Nature Machine Intelligence. Needs Python.

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.

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.

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.