Write scientific preprints in Markdown. Generate professional academic preprint PDFs through automated workflows.¶

🚀 Quick Start¶

Basic workflow:

# Install rxiv-maker
pipx install rxiv-maker

# Check dependencies
rxiv check-installation

# Create manuscript
rxiv init my-paper
cd my-paper

# Generate PDF
rxiv pdf

Complete Installation Guide →

✨ Why Rxiv-Maker?¶

• Write in Markdown: Focus on content, not LaTeX formatting
• Automated Figures: Python/R scripts become publication figures
• Smart Citations: BibTeX integration with cross-references and DOI resolution
• Dual Output: Generate both PDF and DOCX from the same source
• Git-Friendly: Version control for manuscripts and figures
• Reproducible: All figures generated from code
• arXiv Ready: Generate submission packages automatically
• Track Changes: Visual diff between manuscript versions

🔥 Key Features¶

🎨 Enhanced Markdown¶

Write scientific manuscripts using familiar Markdown with useful extensions:

• Scientific cross-references - @fig:plot, @eq:formula, @table:results
• Auto-numbered elements - Figures, tables, and equations number themselves
• Mathematical notation - LaTeX math syntax for beautiful equations
• Code syntax highlighting - Perfect for methodology sections

See Figure @fig:analysis for detailed results. The correlation
coefficient (r = 0.85, *p* < 0.001) demonstrates...

![Analysis Results](FIGURES/scatter_plot.py)
{#fig:analysis}

📚 Citation Management¶

Straightforward bibliography handling:

• BibTeX integration with simple [@citation] syntax
• Automatic bibliography generation in any style
• Multiple citation formats (APA, Nature, IEEE, custom)
• CrossRef DOI resolution for easy reference import

Previous studies [@smith2023; @jones2024] have shown...

## References
<!-- Bibliography automatically generated -->

📊 Automated Figure Generation¶

Transform your analysis scripts into publication-ready figures:

• Python/R script execution during PDF generation
• Version-controlled figures that update with your data
• Matplotlib, ggplot2, Seaborn - use any visualization library
• Intelligent caching for efficient rebuilds

# FIGURES/analysis_plot.py
import matplotlib.pyplot as plt
import pandas as pd

df = pd.read_csv("data/experiment.csv")
plt.figure(figsize=(8, 6))
plt.scatter(df['x'], df['y'])
plt.savefig('analysis_plot.png', dpi=300)

🛠️ VS Code Extension¶

Professional writing environment with intelligent assistance:

• Smart syntax highlighting for enhanced Markdown
• Citation autocompletion from your BibTeX files
• Cross-reference validation and navigation
• One-click PDF generation with build progress

Install VS Code Extension →

🐍 Executable Python Code (Advanced)¶

For dynamic manuscripts that update with your data:

{{py:exec
import pandas as pd
import numpy as np
df = pd.read_csv("FIGURES/DATA/results.csv")
sample_size = len(df)
mean_value = np.mean(df['measurement'])
}}

Our analysis of {{py:get sample_size}} samples shows
mean = {{py:get mean_value:.2f}} units.

Live data integration - Your manuscript updates automatically when data changes.

⚡ Direct LaTeX Injection (Expert)¶

For researchers who need precise typographic control:

Advanced notation: {{tex: $\langle\psi|\phi\rangle$}}

Scientific units: {{tex: \SI{273.15}{\kelvin}}}

Seamlessly blend Markdown simplicity with LaTeX power when you need it.

📝 Use Cases¶

Rxiv-Maker is designed specifically for scientific preprint creation:

• 📄 arXiv Preprints - Physics, mathematics, computer science submissions
• 📄 bioRxiv Preprints - Biology and life sciences submissions
• 📄 medRxiv Preprints - Medical and health sciences submissions
• 📄 Other Preprint Servers - ChemRxiv, PsyArXiv, and more

🤝 Community & Support¶

📄 Citation¶

If Rxiv-Maker helps your research, please cite:

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

📚 Publications Showcase¶

See how researchers are using Rxiv-Maker to create professional manuscripts across diverse scientific fields—from biology and proteomics to computational frameworks.