Scientific publishing increasingly relies on preprint servers for rapid dissemination, yet researchers often struggle with manuscript preparation and quality control. Here we present Rxiv-Maker, a GitHub-native framework that converts markdown content to publication-ready PDFs through automated LaTeX processing. The system addresses reproducibility challenges in computational biology and imaging research by treating manuscripts as executable outputs rather than static documents. Rxiv-Maker integrates version control workflows with automated build environments, enabling collaborative manuscript development whilst maintaining computational provenance. The framework supports programmatic figure generation, essential for microscopy and image analysis workflows where visualisations must reflect current data and processing algorithms. This manuscript, generated entirely using Rxiv-Maker, demonstrates the system's capacity to bridge accessible authoring with professional typesetting, offering researchers a transparent pathway from data to publication that aligns with open science principles.

Rxiv-Maker Rxiv-Maker is an automated LaTeX article generation system that transforms scientific writing from chaos to clarity. It converts Markdown manuscripts into publication-ready PDFs with reproducible figures, professional typesetting, and zero LaTeX hassle. The platform bridges the gap between easy writing (Markdown) and beautiful output (LaTeX), featuring automated figure generation from Python scripts and Mermaid diagrams, seamless citation management, and integration with GitHub Actions for cloud-based PDF generation. Rxiv-Maker enhances the capabilities of traditional scientific writing by ensuring version control compatibility, facilitating reproducible science workflows, and providing professional formatting that meets publication standards.