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.

Official OpenBB MCP server exposing the OpenBB Platform's equity, ETF, macroeconomic, crypto and news data to agents; enable only the tool categories you need to save context. Needs uv locally; some data sources need your own API keys. Not investment advice.

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.

For preclinical life sciences research: bundles MCP connectors for PubMed, bioRxiv, ChEMBL, Open Targets, ClinicalTrials and more, plus analysis skills for single-cell RNA QC, scvi-tools and nf-core pipelines. Official from Anthropic; some data sources need accounts.

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+.

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.

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 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.

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.

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.

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.

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.

Fast Rust toolkit for tabular data with nearly 80 subcommands for querying, stats, cleaning, validation, joins and format conversion on CSV and Excel. Also offers an MCP server and a Claude Cowork plugin.

550+ medical research skills from AIPOCH: PubMed search strategy, study design and sample size, statistics and bioinformatics, journal writing and reviewer responses, all vetted by MedSkillAudit. Some need Python/R or database credentials; have researchers and clinicians review results.

MathWorks' official server that lets agents start your local MATLAB, write and run scripts and unit tests, and check code style and potential errors, for computing, simulation and data analysis. Needs a licensed MATLAB R2021a+ and the downloaded server binary.

Econometrician Pedro Sant'Anna's academic Claude Code setup (fork the repo to use it): Beamer/Quarto lecture slides, paper review and mock refereeing, R/Python analysis and replication packages, with specialist subagents and quality gates. Needs Git and Python; slides need XeLaTeX and Quarto.

Self-hosted engine that maps lab results, checkup reports and wearable data to standard metrics so agents can chart trends, citing the source file for every number. uvx mirobody mcp gives the coding tools; full records need Docker and an LLM API key. A doctor should review results.

Connects agents to live Jupyter notebooks: read, write, insert and execute cells and read multimodal outputs like charts, for interactive data analysis. Bring your own JupyterLab or JupyterHub; open source, maintained by Datalayer.

MathWorks' official toolkit: set up the MCP server via the MATLAB installer so agents can run code, run tests and do static checks; domain skill sets for signal processing, controls, statistics and machine learning install as Claude Code plugins. Needs MATLAB R2021a+.

Official DuckDB skills: query local or S3 CSV, Parquet, Excel and JSON files with SQL or plain language, attach databases, convert formats, analyze spatial data and look up documentation. Needs the DuckDB CLI; tested only on macOS and Linux.

Connects Stata to VS Code or Cursor and exposes a local MCP endpoint so Claude Code or Codex can write and run do-files and read regression output, with graphs shown in the editor; for empirical research. Needs a licensed Stata 17+, the extension installed and the editor open.

Two skills for the MCM/ICM and China's CUMCM math modeling contests: solver breaks down problems, picks models from a 95+ scenario decision matrix and gives Python or MATLAB templates; paper coaches abstracts, model validation and formatting from winning papers. Needs Python or MATLAB.

59 clinical research skills from a radiologist at Korea's Asan Medical Center: study design and sample size, de-identification, statistical figures, 49 reporting guidelines, risk-of-bias checks, citation verification and reviewer replies. Literature APIs need no key. Medical review required.