# Tools

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Resources for Data analysis or Research / Academia, Tagged `python`: 70 items.

> - Data analysis: Querying, statistical analysis, reporting and visualization.
> - Research / Academia: Literature search and reviews, experimental data analysis, paper writing and submission.

- [yt-dlp](https://hebbmind.com/fr/cli/yt-dlp.md): [CLI] Command-line audio and video downloader supporting thousands of sites: pick formats and quality, grab subtitles and metadata, and merge or transcode with FFmpeg. The actively maintained fork of youtube-dl.
- [MarkItDown-MCP](https://hebbmind.com/fr/mcp/markitdown-mcp.md): [MCP] From Microsoft: converts PDF, Word, Excel, PowerPoint, HTML and other files or URLs to Markdown so agents can read and search them. A single convert_to_markdown tool over STDIO or local HTTP.
- [MarkItDown](https://hebbmind.com/fr/cli/markitdown.md): [CLI] Converts PDF, Word, Excel, PowerPoint, HTML, images, audio and more into Markdown that keeps headings, lists and tables, ready for LLMs to read and analyze. Maintained by Microsoft; requires Python 3.10+.
- [PDF](https://hebbmind.com/fr/skill/pdf.md): [Skill] Extracts text and tables from PDFs; merges, splits and rotates pages, adds watermarks, fills forms and OCRs scanned documents. The official Anthropic skill behind Claude's document features; source-available, not open source.
- [Scientific Agent Skills](https://hebbmind.com/fr/skill/scientific-agent-skills.md): [Skill] 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.
- [Browser Use MCP](https://hebbmind.com/fr/mcp/browser-use-mcp.md): [MCP] 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.
- [Fetch MCP Server](https://hebbmind.com/fr/mcp/fetch.md): [MCP] Official MCP reference server that fetches web pages and converts them to Markdown for the model, reading long pages in chunks from a given offset. Zero config, but it can reach internal network addresses, so use it with care.
- [PaddleOCR MCP Server](https://hebbmind.com/fr/mcp/paddlepaddle-mcp-server.md): [MCP] Official PaddleOCR MCP: text recognition and layout parsing for images and PDFs (PP-OCR, PP-StructureV3, PaddleOCR-VL), returning text or Markdown. Runs inference locally, or calls the official API or a self-hosted service.
- [Scrapling](https://hebbmind.com/fr/mcp/scrapling.md): [MCP] 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.
- [Scrapling](https://hebbmind.com/fr/cli/scrapling.md): [CLI] 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.
- [Crawl4AI](https://hebbmind.com/fr/cli/crawl4ai.md): [CLI] 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.
- [OpenBB Platform CLI](https://hebbmind.com/fr/cli/openbb-finance-cli.md): [CLI] 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.
- [Docling](https://hebbmind.com/fr/cli/docling.md): [CLI] Parses PDF, DOCX, PPTX, XLSX, HTML, images and audio, recovering layout, reading order, tables and formulas, and exports Markdown, HTML or lossless JSON. Started by IBM Research, now hosted by the LF AI & Data Foundation; runs fully locally.
- [Scanpy Single-Cell Analysis](https://hebbmind.com/fr/skill/scanpy.md): [Skill] 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.
- [Statistical Analysis](https://hebbmind.com/fr/skill/statistical-analysis.md): [Skill] 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.
- [Qlib](https://hebbmind.com/fr/cli/qlib.md): [CLI] Microsoft's open-source AI quant investment research platform: the qrun command runs dataset building, model training, backtesting and evaluation from a YAML config, with many benchmark models. The official dataset is paused, so prepare market data per the README first.
- [Manim](https://hebbmind.com/fr/cli/manim.md): [CLI] Engine for math and explainer animations in Python (Community Edition, ManimCE): write scenes and render them to video with the manim command, letting agents create teaching and science animations. On macOS install cairo and pkg-config first; formulas need LaTeX.
- [Marker](https://hebbmind.com/fr/cli/marker.md): [CLI] Converts PDFs, images, PPTX, DOCX, XLSX, EPUB and more into Markdown, JSON or HTML, preserving tables, formulas and layout, with optional LLM help for higher accuracy. Needs Python 3.10+ and PyTorch; large-scale commercial use of the model weights needs a paid license.
- [OCRmyPDF](https://hebbmind.com/fr/cli/ocrmypdf.md): [CLI] Adds a searchable, copyable text layer to scanned PDFs, with automatic deskew, rotation and size optimization, outputting PDF/A by default. Built on Tesseract, supports 100+ languages and runs fully locally.
- [book-to-skill](https://hebbmind.com/fr/skill/book-to-skill.md): [Skill] Distills technical books, doc folders or paper collections (PDF, EPUB, DOCX, Markdown and more) into an agent skill with a core framework, on-demand chapter files, glossary and cheat sheet for lookup while working. Extraction needs local Python; poppler or docling optional for PDFs.
- [WhisperX](https://hebbmind.com/fr/cli/whisperx.md): [CLI] Fast speech transcription built on faster-whisper, with word-level timestamps and speaker diarization, suited to meeting notes and subtitles. Diarization needs a Hugging Face token; GPU acceleration needs CUDA.
- [notebooklm-py](https://hebbmind.com/fr/cli/notebooklm-py.md): [CLI] Unofficial Python library and CLI for driving Google NotebookLM (now Gemini Notebook): bulk-import sources, ask cited questions, and generate and download podcasts, videos, slides, quizzes and flashcards. Ships an agent skill. Relies on undocumented APIs and needs a Google sign-in.
- [RenderCV](https://hebbmind.com/fr/cli/rendercv.md): [CLI] Write your resume in YAML and render a cleanly typeset PDF from the command line: multiple themes, fine control of margins, colors and fonts, strict field validation and multi-language support. A companion agent skill is available. Needs Python 3.12+.
- [DVC](https://hebbmind.com/fr/cli/dvc.md): [CLI] Version datasets and models the way Git versions code: data lives in remote storage like S3 or GCS while versions are tracked in your Git repo. Also offers reproducible pipelines and local experiment tracking, rerunning only the steps affected by a change.
- [LLM](https://hebbmind.com/fr/cli/llm.md): [CLI] 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.
- [Trae Agent](https://hebbmind.com/fr/cli/trae-agent.md): [CLI] ByteDance's open-source, general software engineering agent: trae-cli edits files and runs commands from natural language, supports multiple model providers and MCP, and records full execution trajectories. Transparent design suits agent research and customization. Needs your own model API key.
- [mycli](https://hebbmind.com/fr/cli/mycli.md): [CLI] 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.
- [Datasette](https://hebbmind.com/fr/cli/datasette.md): [CLI] 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+.
- [Hugging Face Skills](https://hebbmind.com/fr/skill/huggingface-skills.md): [Skill] Hugging Face's official skills: manage Hub models and datasets with the hf CLI, fine-tune language and vision models, run model evaluations, and build Gradio apps deployed to Spaces. Needs an HF account; cloud training on HF Jobs requires a paid plan.
- [pdfplumber](https://hebbmind.com/fr/cli/pdfplumber.md): [CLI] 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.
- [SQLFluff](https://hebbmind.com/fr/cli/sqlfluff.md): [CLI] 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.
- [BabelDOC](https://hebbmind.com/fr/cli/babeldoc.md): [CLI] 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.
- [PaperQA2](https://hebbmind.com/fr/cli/paper-qa.md): [CLI] 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.
- [VisiData](https://hebbmind.com/fr/cli/visidata.md): [CLI] 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.
- [Scientific Figure Making](https://hebbmind.com/fr/skill/scientific-figure-making.md): [Skill] 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.
- [OpenCompass](https://hebbmind.com/fr/cli/opencompass.md): [CLI] 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.
- [Jupyter Notebooks](https://hebbmind.com/fr/skill/jupyter-notebook.md): [Skill] 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.
- [Life Science Research](https://hebbmind.com/fr/skill/openai-skills-5.md): [Skill] 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.
- [Trafilatura](https://hebbmind.com/fr/cli/trafilatura.md): [CLI] 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.
- [Argos Translate](https://hebbmind.com/fr/cli/argos-translate.md): [CLI] 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.
- [csvkit](https://hebbmind.com/fr/cli/csvkit.md): [CLI] 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.
- [proselint](https://hebbmind.com/fr/cli/proselint.md): [CLI] English prose linter that turns usage guides such as Garner's and advice from great writers into rules, flagging clichés, redundancy, bad comparisons and usage errors line by line, with JSON output for agents. Runs locally with Python; English only.
- [mcp-obsidian](https://hebbmind.com/fr/mcp/mcp-obsidian.md): [MCP] Uses Obsidian's community Local REST API plugin so agents can list, read, search, append to and delete notes, and insert content at a heading, block reference or frontmatter field. Install that plugin and configure its API key first.
- [Excel MCP Server](https://hebbmind.com/fr/mcp/excel-mcp-server.md): [MCP] Create, read and modify xlsx workbooks without Microsoft Excel installed: formulas, formatting and conditional formatting, charts, pivot tables and tables. Runs locally over stdio or as a remote HTTP service.
- [AiPy](https://hebbmind.com/fr/cli/aipyapp.md): [CLI] Knownsec's open-source Python-use agent: describe a task in plain language and it writes and runs Python on your machine, e.g. tidying Excel files, summarizing attendance or screening resumes. Needs Python 3.11+ and a model API key such as DeepSeek; code runs locally, so back up important files.
- [Hugging Face CLI](https://hebbmind.com/fr/cli/huggingface-hub.md): [CLI] Hugging Face's official hf CLI: search, download and upload models and datasets, manage repos and storage buckets, and run jobs on Hugging Face's cloud. Output adapts automatically for agents, and hf skills add installs companion skills. Uploads and similar actions need a login.
- [Camelot](https://hebbmind.com/fr/cli/camelot.md): [CLI] Open-source PDF table extraction with a camelot CLI: exports tables from financial reports, bank statements and statistical reports to Excel, CSV or Markdown, with an accuracy score. Needs Python 3.10+; handles text-based PDFs by default, scans need the ml and ocr extras. Double-check results.
- [SQLMesh](https://hebbmind.com/fr/cli/sqlmesh.md): [CLI] Framework for writing data transformation models in SQL or Python, with a Terraform-like plan/apply flow, virtual data environments, unit tests and table diffs, and transpilation across 10+ SQL dialects. A Linux Foundation project and an alternative to dbt.
- [Pix2Text](https://hebbmind.com/fr/cli/pix2text.md): [CLI] Recognizes images or whole PDFs (including scans) with math formulas and tables into Markdown and LaTeX, strong on English and Chinese and supporting 80+ languages, handy for digitizing exams, lecture notes and study notes. An open-source Mathpix alternative that runs locally with Python.
- [Paper Search MCP](https://hebbmind.com/fr/mcp/paper-search-mcp.md): [MCP] Unified search across 20+ academic sources including arXiv, PubMed, bioRxiv, Semantic Scholar and OpenAlex, returning deduplicated, normalized results and downloading full text via open-access channels first. Most sources need no API key.

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