rxiv-maker 1.21.0

Write scientific preprints in Markdown. Generate publication-ready PDFs efficiently.

Rxiv-Maker

Rxiv-Maker converts enhanced Markdown into professional PDFs with automated figure generation, citation management, and LaTeX typesetting. Write in Markdown, get publication-ready output for arXiv, bioRxiv, and other preprint servers.

Installation

macOS (includes LaTeX automatically):

brew install henriqueslab/formulas/rxiv-maker

Linux / Windows (WSL):

pipx install rxiv-maker    # or: uv tool install rxiv-maker

Verify setup:

rxiv check-installation

LaTeX is required. See the installation guide for platform-specific LaTeX instructions.

Quick Start

rxiv init my-paper
cd my-paper
rxiv pdf

To explore a complete working example:

rxiv get-rxiv-preprint
cd manuscript-rxiv-maker/MANUSCRIPT
rxiv pdf

Features

• Enhanced Markdown - Scientific cross-references (@fig:plot, @eq:formula), auto-numbered figures/tables/equations, LaTeX math
• Automated figures - Python and R scripts executed during PDF generation, with intelligent caching
• Executable code blocks - Jupyter-like {{py:exec}} and {{py:get variable}} for live data in manuscripts
• Citation management - BibTeX with [@citation] syntax, multiple styles, inline DOI resolution
• Dual output - PDF and DOCX from the same source
• arXiv/bioRxiv submission - Generate submission packages automatically
• Track changes - Visual diff between manuscript versions
• VS Code extension - Syntax highlighting, citation autocompletion, one-click builds

Documentation

rxiv-maker.henriqueslab.org - Installation, guides, CLI reference, troubleshooting.

For contributors: CONTRIBUTING.md

Ecosystem

Repository	Purpose
rxiv-maker	Core CLI tool
docker-rxiv-maker	Pre-configured container with LaTeX
manuscript-rxiv-maker	Complete example (arXiv:2508.00836)
vscode-rxiv-maker	VS Code extension

Publications

Publication	Venue
Rxiv-Maker: an automated template engine for streamlined scientific publications	arXiv (2025)
Customizable FDM-based zebrafish embryo mold for live imaging	bioRxiv (2025)
mAIcrobe: an open-source framework for high-throughput bacterial image analysis	bioRxiv (2025)
Filopodome proteomics identifies CCT8 as a MYO10 interactor critical for filopodia functions	bioRxiv (2025)
EZInput: A Cross-Environment Python Library for Easy UI Generation in Scientific Computing	arXiv (2026)
Packaging Jupyter notebooks as installable desktop apps using LabConstrictor	arXiv (2026)

Using Rxiv-Maker for your research? Let us know.

Community

• GitHub Discussions - Questions and tips
• Issues - Bug reports and feature requests
• Google Colab - Try without installing

Citation

@misc{saraiva_2025_rxivmaker,
  title={Rxiv-Maker: an automated template engine for streamlined scientific publications},
  author={Bruno M. Saraiva and Ant\'{o}nio D. Brito and Guillaume Jaquemet and Ricardo Henriques},
  year={2025},
  eprint={2508.00836},
  archivePrefix={arXiv},
  url={https://arxiv.org/abs/2508.00836}
}

License

MIT License - see LICENSE for details.